Data analysis for Optimization of SNV calling, synthetic influenza RNA part
Bessie Wang
6/14/2022
This notebook generates the following figures for the manuscript:
- Figure 3A (influenza)
- Figure 3B
- Figure 4C
- Figure 4D
- Supp. Fig5A
- Supp. Fig5C
- Supp. Fig5D
- Supp. Fig5E
- Supp. Fig6B
- Supp. Fig6C
- Supp. Fig7A
- Supp. Fig7B
- Supp. Fig7C
- Supp. Fig8C
- Supp. Fig8D
Required inputs to run notebook:
R functions:
- maf_functions.R ## Input SNV file:
- SNV_info_allcaller.csv
- SNV_info_with_transcriptionerror_binom.csv ## Metadata outlining samples within the matrix
- Edited_metadata.csv
# Load necessary packages
library('ggplot2')
library('plyr')
library('tidyverse')## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──## ✓ tibble 3.1.1 ✓ dplyr 1.0.7
## ✓ tidyr 1.1.3 ✓ stringr 1.4.0
## ✓ readr 2.0.1 ✓ forcats 0.5.1
## ✓ purrr 0.3.4## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::arrange() masks plyr::arrange()
## x purrr::compact() masks plyr::compact()
## x dplyr::count() masks plyr::count()
## x dplyr::failwith() masks plyr::failwith()
## x dplyr::filter() masks stats::filter()
## x dplyr::id() masks plyr::id()
## x dplyr::lag() masks stats::lag()
## x dplyr::mutate() masks plyr::mutate()
## x dplyr::rename() masks plyr::rename()
## x dplyr::summarise() masks plyr::summarise()
## x dplyr::summarize() masks plyr::summarize()library('dplyr')
library('glue')
library('vcfR')##
## ***** *** vcfR *** *****
## This is vcfR 1.12.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****library('tools')
library('seqinr')##
## Attaching package: 'seqinr'## The following object is masked from 'package:vcfR':
##
## write.fasta## The following object is masked from 'package:dplyr':
##
## count## The following object is masked from 'package:plyr':
##
## countlibrary('plotly')##
## Attaching package: 'plotly'## The following objects are masked from 'package:plyr':
##
## arrange, mutate, rename, summarise## The following object is masked from 'package:ggplot2':
##
## last_plot## The following object is masked from 'package:stats':
##
## filter## The following object is masked from 'package:graphics':
##
## layoutSet working directory
workdirectory= "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols/" # set this as its own variable so it is super easy to change later
knitr::opts_knit$set(root.dir = workdirectory) # this should set the rmd root directory so you don't have to type out 'workdirectory' later on (you still can if you want it doesn't matter)
getwd() # this should tell you what directory you are working in## [1] "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols"#load vivaldi scripts (process all the vcf files and output a single dataframe)
source(glue('{workdirectory}scripts/maf_functions/read_reference_fasta_dna.R'))
source(glue('{workdirectory}scripts/maf_functions/arrange_gt_data.R'))
source(glue('{workdirectory}scripts/maf_functions/arrange_no_gt_data.R'))
source(glue('{workdirectory}scripts/maf_functions/arrange_gt_varscan.R'))
source(glue('{workdirectory}scripts/maf_functions/add_metadata.R'))
source(glue('{workdirectory}scripts/maf_functions/filter_variants.R'))
source(glue('{workdirectory}scripts/maf_functions/prepare_annotations.R'))
source(glue('{workdirectory}scripts/maf_functions/snpeff_info.R'))
source(glue('{workdirectory}scripts/maf_functions/shannon_entropy.R'))
source(glue('{workdirectory}scripts/maf_functions/plot_shannon.R'))
source(glue('{workdirectory}scripts/maf_functions/tally_it.R'))
source(glue('{workdirectory}scripts/maf_functions/tstv_ratio.R'))
source(glue('{workdirectory}scripts/maf_functions/tstv_plot.R'))
source(glue('{workdirectory}scripts/maf_functions/snv_location.R'))Run arrange_gt_data on ivar, timo, haplotypecaller, mutect2, freebayes data under standard setting
vcf_df = arrange_gt_data( glue('{workdirectory}/analysis_final/'), glue('{workdirectory}/analysis_final/Reference_coding.fa'), annotated = 'no', ntlist=c('A','G','T','C'))## Number of chroms in fasta: 3## Length of input files: 485## Input vcf files include: c("/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_ivar_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_hc_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_timo_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_freebayes_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_mutect2_standard_unfiltered.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_timo_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_freebayes_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_hc_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_ivar_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_mutect2_standard_unfiltered.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//analysis_final//000000000-K4LKV_l01_undetermined.fas_BWA_timo_standard.vcf")## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 208
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 208
## Character matrix gt cols: 10
## skip: 0
## nrows: 208
## row_num: 0
##
Processed variant: 208
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 581
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 581
## Character matrix gt cols: 10
## skip: 0
## nrows: 581
## row_num: 0
##
Processed variant: 581
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 166
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 166
## Character matrix gt cols: 10
## skip: 0
## nrows: 166
## row_num: 0
##
Processed variant: 166
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 363
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 363
## Character matrix gt cols: 10
## skip: 0
## nrows: 363
## row_num: 0
##
Processed variant: 363
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 47
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 158
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 158
## Character matrix gt cols: 10
## skip: 0
## nrows: 158
## row_num: 0
##
Processed variant: 158
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 575
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 575
## Character matrix gt cols: 10
## skip: 0
## nrows: 575
## row_num: 0
##
Processed variant: 575
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 144
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 144
## Character matrix gt cols: 10
## skip: 0
## nrows: 144
## row_num: 0
##
Processed variant: 144
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 370
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 370
## Character matrix gt cols: 10
## skip: 0
## nrows: 370
## row_num: 0
##
Processed variant: 370
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 46
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 0
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_freebayes_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 0
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_hc_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 0
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_ivar_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 0
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_mutect2_standard_unfiltered## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 0
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_timo_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 4
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 4
## Character matrix gt cols: 10
## skip: 0
## nrows: 4
## row_num: 0
##
Processed variant: 4
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## No snps for sample: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_freebayes_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 10
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 10
## Character matrix gt cols: 10
## skip: 0
## nrows: 10
## row_num: 0
##
Processed variant: 10
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 0
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_ivar_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 12
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 12
## Character matrix gt cols: 10
## skip: 0
## nrows: 12
## row_num: 0
##
Processed variant: 12
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 0
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_timo_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 47
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 41
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 41
## Character matrix gt cols: 10
## skip: 0
## nrows: 41
## row_num: 0
##
Processed variant: 41
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 0
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## No variant data: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_freebayes_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 0
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## No variant data: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_hc_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 0
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_ivar_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 1
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1
## Character matrix gt cols: 10
## skip: 0
## nrows: 1
## row_num: 0
##
Processed variant: 1
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 1
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1
## Character matrix gt cols: 10
## skip: 0
## nrows: 1
## row_num: 0
##
Processed variant: 1
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 4
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 4
## Character matrix gt cols: 10
## skip: 0
## nrows: 4
## row_num: 0
##
Processed variant: 4
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 3
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 3
## Character matrix gt cols: 10
## skip: 0
## nrows: 3
## row_num: 0
##
Processed variant: 3
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 0
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_ivar_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 5
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 5
## Character matrix gt cols: 10
## skip: 0
## nrows: 5
## row_num: 0
##
Processed variant: 5
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 2
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 2
## Character matrix gt cols: 10
## skip: 0
## nrows: 2
## row_num: 0
##
Processed variant: 2
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 0
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_freebayes_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 0
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_hc_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 0
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_ivar_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 0
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_mutect2_standard_unfiltered## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 0
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_timo_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 51
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 79
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 79
## Character matrix gt cols: 10
## skip: 0
## nrows: 79
## row_num: 0
##
Processed variant: 79
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 100
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 100
## Character matrix gt cols: 10
## skip: 0
## nrows: 100
## row_num: 0
##
Processed variant: 100
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 35
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 35
## Character matrix gt cols: 10
## skip: 0
## nrows: 35
## row_num: 0
##
Processed variant: 35
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 72
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 72
## Character matrix gt cols: 10
## skip: 0
## nrows: 72
## row_num: 0
##
Processed variant: 72
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 46
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 75
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 75
## Character matrix gt cols: 10
## skip: 0
## nrows: 75
## row_num: 0
##
Processed variant: 75
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 46
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 83
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 83
## Character matrix gt cols: 10
## skip: 0
## nrows: 83
## row_num: 0
##
Processed variant: 83
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 126
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 126
## Character matrix gt cols: 10
## skip: 0
## nrows: 126
## row_num: 0
##
Processed variant: 126
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 46
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 63
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 63
## Character matrix gt cols: 10
## skip: 0
## nrows: 63
## row_num: 0
##
Processed variant: 63
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 110
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 110
## Character matrix gt cols: 10
## skip: 0
## nrows: 110
## row_num: 0
##
Processed variant: 110
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 37
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 10
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 47
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 75
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 75
## Character matrix gt cols: 10
## skip: 0
## nrows: 75
## row_num: 0
##
Processed variant: 75
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 68
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 68
## Character matrix gt cols: 10
## skip: 0
## nrows: 68
## row_num: 0
##
Processed variant: 68
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 46
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 43
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 82
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 82
## Character matrix gt cols: 10
## skip: 0
## nrows: 82
## row_num: 0
##
Processed variant: 82
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 44
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 91
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 91
## Character matrix gt cols: 10
## skip: 0
## nrows: 91
## row_num: 0
##
Processed variant: 91
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 17
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 17
## Character matrix gt cols: 10
## skip: 0
## nrows: 17
## row_num: 0
##
Processed variant: 17
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 42
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 82
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 82
## Character matrix gt cols: 10
## skip: 0
## nrows: 82
## row_num: 0
##
Processed variant: 82
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 90
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 90
## Character matrix gt cols: 10
## skip: 0
## nrows: 90
## row_num: 0
##
Processed variant: 90
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 38
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 76
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 76
## Character matrix gt cols: 10
## skip: 0
## nrows: 76
## row_num: 0
##
Processed variant: 76
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 38
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 73
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 10
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 11
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 11
## Character matrix gt cols: 10
## skip: 0
## nrows: 11
## row_num: 0
##
Processed variant: 11
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 43
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 73
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 10
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 89
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 89
## Character matrix gt cols: 10
## skip: 0
## nrows: 89
## row_num: 0
##
Processed variant: 89
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 58
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 58
## Character matrix gt cols: 10
## skip: 0
## nrows: 58
## row_num: 0
##
Processed variant: 58
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 76
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 76
## Character matrix gt cols: 10
## skip: 0
## nrows: 76
## row_num: 0
##
Processed variant: 76
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 40
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 40
## Character matrix gt cols: 10
## skip: 0
## nrows: 40
## row_num: 0
##
Processed variant: 40
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 43
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 117
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 117
## Character matrix gt cols: 10
## skip: 0
## nrows: 117
## row_num: 0
##
Processed variant: 117
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 144
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 144
## Character matrix gt cols: 10
## skip: 0
## nrows: 144
## row_num: 0
##
Processed variant: 144
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 41
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 41
## Character matrix gt cols: 10
## skip: 0
## nrows: 41
## row_num: 0
##
Processed variant: 41
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 47
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 67
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 67
## Character matrix gt cols: 10
## skip: 0
## nrows: 67
## row_num: 0
##
Processed variant: 67
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 49
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 74
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 74
## Character matrix gt cols: 10
## skip: 0
## nrows: 74
## row_num: 0
##
Processed variant: 74
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 39
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 39
## Character matrix gt cols: 10
## skip: 0
## nrows: 39
## row_num: 0
##
Processed variant: 39
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 79
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 79
## Character matrix gt cols: 10
## skip: 0
## nrows: 79
## row_num: 0
##
Processed variant: 79
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 44
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 116
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 116
## Character matrix gt cols: 10
## skip: 0
## nrows: 116
## row_num: 0
##
Processed variant: 116
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 18
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 18
## Character matrix gt cols: 10
## skip: 0
## nrows: 18
## row_num: 0
##
Processed variant: 18
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 47
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 64
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 10
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 93
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 93
## Character matrix gt cols: 10
## skip: 0
## nrows: 93
## row_num: 0
##
Processed variant: 93
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 42
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 33
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 33
## Character matrix gt cols: 10
## skip: 0
## nrows: 33
## row_num: 0
##
Processed variant: 33
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 78
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 78
## Character matrix gt cols: 10
## skip: 0
## nrows: 78
## row_num: 0
##
Processed variant: 78
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 33
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 33
## Character matrix gt cols: 10
## skip: 0
## nrows: 33
## row_num: 0
##
Processed variant: 33
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 104
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 104
## Character matrix gt cols: 10
## skip: 0
## nrows: 104
## row_num: 0
##
Processed variant: 104
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 12
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 12
## Character matrix gt cols: 10
## skip: 0
## nrows: 12
## row_num: 0
##
Processed variant: 12
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 41
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 41
## Character matrix gt cols: 10
## skip: 0
## nrows: 41
## row_num: 0
##
Processed variant: 41
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 73
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 10
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 94
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 94
## Character matrix gt cols: 10
## skip: 0
## nrows: 94
## row_num: 0
##
Processed variant: 94
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 52
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 52
## Character matrix gt cols: 10
## skip: 0
## nrows: 52
## row_num: 0
##
Processed variant: 52
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 75
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 75
## Character matrix gt cols: 10
## skip: 0
## nrows: 75
## row_num: 0
##
Processed variant: 75
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 51
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 66
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 66
## Character matrix gt cols: 10
## skip: 0
## nrows: 66
## row_num: 0
##
Processed variant: 66
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 37
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 10
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 42
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 61
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 61
## Character matrix gt cols: 10
## skip: 0
## nrows: 61
## row_num: 0
##
Processed variant: 61
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 83
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 83
## Character matrix gt cols: 10
## skip: 0
## nrows: 83
## row_num: 0
##
Processed variant: 83
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 73
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 10
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 101
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 101
## Character matrix gt cols: 10
## skip: 0
## nrows: 101
## row_num: 0
##
Processed variant: 101
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 70
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 70
## Character matrix gt cols: 10
## skip: 0
## nrows: 70
## row_num: 0
##
Processed variant: 70
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 64
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 10
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 41
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 41
## Character matrix gt cols: 10
## skip: 0
## nrows: 41
## row_num: 0
##
Processed variant: 41
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 75
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 75
## Character matrix gt cols: 10
## skip: 0
## nrows: 75
## row_num: 0
##
Processed variant: 75
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 100
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 100
## Character matrix gt cols: 10
## skip: 0
## nrows: 100
## row_num: 0
##
Processed variant: 100
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 38
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 73
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 10
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 42
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 72
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 72
## Character matrix gt cols: 10
## skip: 0
## nrows: 72
## row_num: 0
##
Processed variant: 72
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 20
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 20
## Character matrix gt cols: 10
## skip: 0
## nrows: 20
## row_num: 0
##
Processed variant: 20
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 43
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 68
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 68
## Character matrix gt cols: 10
## skip: 0
## nrows: 68
## row_num: 0
##
Processed variant: 68
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 76
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 76
## Character matrix gt cols: 10
## skip: 0
## nrows: 76
## row_num: 0
##
Processed variant: 76
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 29
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 29
## Character matrix gt cols: 10
## skip: 0
## nrows: 29
## row_num: 0
##
Processed variant: 29
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 66
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 66
## Character matrix gt cols: 10
## skip: 0
## nrows: 66
## row_num: 0
##
Processed variant: 66
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 30
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 30
## Character matrix gt cols: 10
## skip: 0
## nrows: 30
## row_num: 0
##
Processed variant: 30
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 79
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 79
## Character matrix gt cols: 10
## skip: 0
## nrows: 79
## row_num: 0
##
Processed variant: 79
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 11
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 11
## Character matrix gt cols: 10
## skip: 0
## nrows: 11
## row_num: 0
##
Processed variant: 11
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 69
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 69
## Character matrix gt cols: 10
## skip: 0
## nrows: 69
## row_num: 0
##
Processed variant: 69
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 98
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 98
## Character matrix gt cols: 10
## skip: 0
## nrows: 98
## row_num: 0
##
Processed variant: 98
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 48
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 62
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 62
## Character matrix gt cols: 10
## skip: 0
## nrows: 62
## row_num: 0
##
Processed variant: 62
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 62
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 62
## Character matrix gt cols: 10
## skip: 0
## nrows: 62
## row_num: 0
##
Processed variant: 62
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 37
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 10
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 82
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 82
## Character matrix gt cols: 10
## skip: 0
## nrows: 82
## row_num: 0
##
Processed variant: 82
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 69
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 69
## Character matrix gt cols: 10
## skip: 0
## nrows: 69
## row_num: 0
##
Processed variant: 69
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 40
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 40
## Character matrix gt cols: 10
## skip: 0
## nrows: 40
## row_num: 0
##
Processed variant: 40
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 48
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 73
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 10
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 85
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 85
## Character matrix gt cols: 10
## skip: 0
## nrows: 85
## row_num: 0
##
Processed variant: 85
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 40
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 40
## Character matrix gt cols: 10
## skip: 0
## nrows: 40
## row_num: 0
##
Processed variant: 40
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 64
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 10
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 43
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 85
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 85
## Character matrix gt cols: 10
## skip: 0
## nrows: 85
## row_num: 0
##
Processed variant: 85
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 23
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 23
## Character matrix gt cols: 10
## skip: 0
## nrows: 23
## row_num: 0
##
Processed variant: 23
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 69
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 69
## Character matrix gt cols: 10
## skip: 0
## nrows: 69
## row_num: 0
##
Processed variant: 69
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 112
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 112
## Character matrix gt cols: 10
## skip: 0
## nrows: 112
## row_num: 0
##
Processed variant: 112
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 30
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 30
## Character matrix gt cols: 10
## skip: 0
## nrows: 30
## row_num: 0
##
Processed variant: 30
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 69
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 69
## Character matrix gt cols: 10
## skip: 0
## nrows: 69
## row_num: 0
##
Processed variant: 69
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 28
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 28
## Character matrix gt cols: 10
## skip: 0
## nrows: 28
## row_num: 0
##
Processed variant: 28
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 62
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 62
## Character matrix gt cols: 10
## skip: 0
## nrows: 62
## row_num: 0
##
Processed variant: 62
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 11
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 11
## Character matrix gt cols: 10
## skip: 0
## nrows: 11
## row_num: 0
##
Processed variant: 11
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 74
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 74
## Character matrix gt cols: 10
## skip: 0
## nrows: 74
## row_num: 0
##
Processed variant: 74
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 46
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 79
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 79
## Character matrix gt cols: 10
## skip: 0
## nrows: 79
## row_num: 0
##
Processed variant: 79
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 49
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 66
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 66
## Character matrix gt cols: 10
## skip: 0
## nrows: 66
## row_num: 0
##
Processed variant: 66
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 74
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 74
## Character matrix gt cols: 10
## skip: 0
## nrows: 74
## row_num: 0
##
Processed variant: 74
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 37
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 10
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 92
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 92
## Character matrix gt cols: 10
## skip: 0
## nrows: 92
## row_num: 0
##
Processed variant: 92
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 129
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 129
## Character matrix gt cols: 10
## skip: 0
## nrows: 129
## row_num: 0
##
Processed variant: 129
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 49
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 61
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 61
## Character matrix gt cols: 10
## skip: 0
## nrows: 61
## row_num: 0
##
Processed variant: 61
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 77
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 77
## Character matrix gt cols: 10
## skip: 0
## nrows: 77
## row_num: 0
##
Processed variant: 77
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 44
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 81
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 81
## Character matrix gt cols: 10
## skip: 0
## nrows: 81
## row_num: 0
##
Processed variant: 81
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 127
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 127
## Character matrix gt cols: 10
## skip: 0
## nrows: 127
## row_num: 0
##
Processed variant: 127
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 42
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 43
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 78
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 78
## Character matrix gt cols: 10
## skip: 0
## nrows: 78
## row_num: 0
##
Processed variant: 78
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 84
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 84
## Character matrix gt cols: 10
## skip: 0
## nrows: 84
## row_num: 0
##
Processed variant: 84
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 75
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 75
## Character matrix gt cols: 10
## skip: 0
## nrows: 75
## row_num: 0
##
Processed variant: 75
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 90
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 90
## Character matrix gt cols: 10
## skip: 0
## nrows: 90
## row_num: 0
##
Processed variant: 90
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 19
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 19
## Character matrix gt cols: 10
## skip: 0
## nrows: 19
## row_num: 0
##
Processed variant: 19
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 69
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 69
## Character matrix gt cols: 10
## skip: 0
## nrows: 69
## row_num: 0
##
Processed variant: 69
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 73
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 10
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 36
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 36
## Character matrix gt cols: 10
## skip: 0
## nrows: 36
## row_num: 0
##
Processed variant: 36
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 132
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 132
## Character matrix gt cols: 10
## skip: 0
## nrows: 132
## row_num: 0
##
Processed variant: 132
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 37
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 10
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 103
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 103
## Character matrix gt cols: 10
## skip: 0
## nrows: 103
## row_num: 0
##
Processed variant: 103
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 12
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 12
## Character matrix gt cols: 10
## skip: 0
## nrows: 12
## row_num: 0
##
Processed variant: 12
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 43
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 81
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 81
## Character matrix gt cols: 10
## skip: 0
## nrows: 81
## row_num: 0
##
Processed variant: 81
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 104
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 104
## Character matrix gt cols: 10
## skip: 0
## nrows: 104
## row_num: 0
##
Processed variant: 104
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 42
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 49
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 80
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 80
## Character matrix gt cols: 10
## skip: 0
## nrows: 80
## row_num: 0
##
Processed variant: 80
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 52
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 52
## Character matrix gt cols: 10
## skip: 0
## nrows: 52
## row_num: 0
##
Processed variant: 52
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 84
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 84
## Character matrix gt cols: 10
## skip: 0
## nrows: 84
## row_num: 0
##
Processed variant: 84
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 40
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 40
## Character matrix gt cols: 10
## skip: 0
## nrows: 40
## row_num: 0
##
Processed variant: 40
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 94
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 94
## Character matrix gt cols: 10
## skip: 0
## nrows: 94
## row_num: 0
##
Processed variant: 94
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 107
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 107
## Character matrix gt cols: 10
## skip: 0
## nrows: 107
## row_num: 0
##
Processed variant: 107
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 36
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 36
## Character matrix gt cols: 10
## skip: 0
## nrows: 36
## row_num: 0
##
Processed variant: 36
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 95
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 95
## Character matrix gt cols: 10
## skip: 0
## nrows: 95
## row_num: 0
##
Processed variant: 95
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 53
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 53
## Character matrix gt cols: 10
## skip: 0
## nrows: 53
## row_num: 0
##
Processed variant: 53
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 68
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 68
## Character matrix gt cols: 10
## skip: 0
## nrows: 68
## row_num: 0
##
Processed variant: 68
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 42
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 63
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 63
## Character matrix gt cols: 10
## skip: 0
## nrows: 63
## row_num: 0
##
Processed variant: 63
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 44
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 66
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 66
## Character matrix gt cols: 10
## skip: 0
## nrows: 66
## row_num: 0
##
Processed variant: 66
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 16
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 16
## Character matrix gt cols: 10
## skip: 0
## nrows: 16
## row_num: 0
##
Processed variant: 16
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 51
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 108
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 108
## Character matrix gt cols: 10
## skip: 0
## nrows: 108
## row_num: 0
##
Processed variant: 108
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 51
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 78
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 78
## Character matrix gt cols: 10
## skip: 0
## nrows: 78
## row_num: 0
##
Processed variant: 78
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 35
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 35
## Character matrix gt cols: 10
## skip: 0
## nrows: 35
## row_num: 0
##
Processed variant: 35
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 91
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 91
## Character matrix gt cols: 10
## skip: 0
## nrows: 91
## row_num: 0
##
Processed variant: 91
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 38
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 81
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 81
## Character matrix gt cols: 10
## skip: 0
## nrows: 81
## row_num: 0
##
Processed variant: 81
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 12
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 12
## Character matrix gt cols: 10
## skip: 0
## nrows: 12
## row_num: 0
##
Processed variant: 12
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 49
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 139
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 139
## Character matrix gt cols: 10
## skip: 0
## nrows: 139
## row_num: 0
##
Processed variant: 139
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 52
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 52
## Character matrix gt cols: 10
## skip: 0
## nrows: 52
## row_num: 0
##
Processed variant: 52
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 137
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 137
## Character matrix gt cols: 10
## skip: 0
## nrows: 137
## row_num: 0
##
Processed variant: 137
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 46
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 95
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 95
## Character matrix gt cols: 10
## skip: 0
## nrows: 95
## row_num: 0
##
Processed variant: 95
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 52
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 52
## Character matrix gt cols: 10
## skip: 0
## nrows: 52
## row_num: 0
##
Processed variant: 52
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 114
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 114
## Character matrix gt cols: 10
## skip: 0
## nrows: 114
## row_num: 0
##
Processed variant: 114
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 39
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 39
## Character matrix gt cols: 10
## skip: 0
## nrows: 39
## row_num: 0
##
Processed variant: 39
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 48
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 70
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 70
## Character matrix gt cols: 10
## skip: 0
## nrows: 70
## row_num: 0
##
Processed variant: 70
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 64
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 10
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 49
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 127
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 127
## Character matrix gt cols: 10
## skip: 0
## nrows: 127
## row_num: 0
##
Processed variant: 127
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 157
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 157
## Character matrix gt cols: 10
## skip: 0
## nrows: 157
## row_num: 0
##
Processed variant: 157
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 71
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 71
## Character matrix gt cols: 10
## skip: 0
## nrows: 71
## row_num: 0
##
Processed variant: 71
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 88
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 88
## Character matrix gt cols: 10
## skip: 0
## nrows: 88
## row_num: 0
##
Processed variant: 88
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 42
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 120
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 120
## Character matrix gt cols: 10
## skip: 0
## nrows: 120
## row_num: 0
##
Processed variant: 120
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 49
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 139
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 139
## Character matrix gt cols: 10
## skip: 0
## nrows: 139
## row_num: 0
##
Processed variant: 139
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 44
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 68
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 68
## Character matrix gt cols: 10
## skip: 0
## nrows: 68
## row_num: 0
##
Processed variant: 68
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 43
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 77
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 77
## Character matrix gt cols: 10
## skip: 0
## nrows: 77
## row_num: 0
##
Processed variant: 77
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 16
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 16
## Character matrix gt cols: 10
## skip: 0
## nrows: 16
## row_num: 0
##
Processed variant: 16
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 164
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 164
## Character matrix gt cols: 10
## skip: 0
## nrows: 164
## row_num: 0
##
Processed variant: 164
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 51
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 156
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 156
## Character matrix gt cols: 10
## skip: 0
## nrows: 156
## row_num: 0
##
Processed variant: 156
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 31
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 31
## Character matrix gt cols: 10
## skip: 0
## nrows: 31
## row_num: 0
##
Processed variant: 31
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 92
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 92
## Character matrix gt cols: 10
## skip: 0
## nrows: 92
## row_num: 0
##
Processed variant: 92
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 33
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 33
## Character matrix gt cols: 10
## skip: 0
## nrows: 33
## row_num: 0
##
Processed variant: 33
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 61
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 61
## Character matrix gt cols: 10
## skip: 0
## nrows: 61
## row_num: 0
##
Processed variant: 61
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 11
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 11
## Character matrix gt cols: 10
## skip: 0
## nrows: 11
## row_num: 0
##
Processed variant: 11
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 74
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 74
## Character matrix gt cols: 10
## skip: 0
## nrows: 74
## row_num: 0
##
Processed variant: 74
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 46
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 115
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 115
## Character matrix gt cols: 10
## skip: 0
## nrows: 115
## row_num: 0
##
Processed variant: 115
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 76
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 76
## Character matrix gt cols: 10
## skip: 0
## nrows: 76
## row_num: 0
##
Processed variant: 76
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 80
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 80
## Character matrix gt cols: 10
## skip: 0
## nrows: 80
## row_num: 0
##
Processed variant: 80
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 53
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 53
## Character matrix gt cols: 10
## skip: 0
## nrows: 53
## row_num: 0
##
Processed variant: 53
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 73
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 10
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 77
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 77
## Character matrix gt cols: 10
## skip: 0
## nrows: 77
## row_num: 0
##
Processed variant: 77
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 103
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 103
## Character matrix gt cols: 10
## skip: 0
## nrows: 103
## row_num: 0
##
Processed variant: 103
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 39
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 39
## Character matrix gt cols: 10
## skip: 0
## nrows: 39
## row_num: 0
##
Processed variant: 39
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 51
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 117
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 117
## Character matrix gt cols: 10
## skip: 0
## nrows: 117
## row_num: 0
##
Processed variant: 117
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 54
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 54
## Character matrix gt cols: 10
## skip: 0
## nrows: 54
## row_num: 0
##
Processed variant: 54
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 89
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 89
## Character matrix gt cols: 10
## skip: 0
## nrows: 89
## row_num: 0
##
Processed variant: 89
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 42
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 72
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 72
## Character matrix gt cols: 10
## skip: 0
## nrows: 72
## row_num: 0
##
Processed variant: 72
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 45
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 98
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 98
## Character matrix gt cols: 10
## skip: 0
## nrows: 98
## row_num: 0
##
Processed variant: 98
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 19
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 19
## Character matrix gt cols: 10
## skip: 0
## nrows: 19
## row_num: 0
##
Processed variant: 19
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 47
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 95
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 95
## Character matrix gt cols: 10
## skip: 0
## nrows: 95
## row_num: 0
##
Processed variant: 95
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 49
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 128
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 128
## Character matrix gt cols: 10
## skip: 0
## nrows: 128
## row_num: 0
##
Processed variant: 128
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 40
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 40
## Character matrix gt cols: 10
## skip: 0
## nrows: 40
## row_num: 0
##
Processed variant: 40
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 141
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 141
## Character matrix gt cols: 10
## skip: 0
## nrows: 141
## row_num: 0
##
Processed variant: 141
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 41
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 41
## Character matrix gt cols: 10
## skip: 0
## nrows: 41
## row_num: 0
##
Processed variant: 41
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 162
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 162
## Character matrix gt cols: 10
## skip: 0
## nrows: 162
## row_num: 0
##
Processed variant: 162
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 16
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 16
## Character matrix gt cols: 10
## skip: 0
## nrows: 16
## row_num: 0
##
Processed variant: 16
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 126
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 126
## Character matrix gt cols: 10
## skip: 0
## nrows: 126
## row_num: 0
##
Processed variant: 126
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 50
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 98
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 98
## Character matrix gt cols: 10
## skip: 0
## nrows: 98
## row_num: 0
##
Processed variant: 98
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 51
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 91
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 91
## Character matrix gt cols: 10
## skip: 0
## nrows: 91
## row_num: 0
##
Processed variant: 91
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 53
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 53
## Character matrix gt cols: 10
## skip: 0
## nrows: 53
## row_num: 0
##
Processed variant: 53
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 94
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 94
## Character matrix gt cols: 10
## skip: 0
## nrows: 94
## row_num: 0
##
Processed variant: 94
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 40
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 40
## Character matrix gt cols: 10
## skip: 0
## nrows: 40
## row_num: 0
##
Processed variant: 40
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 49
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 85
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 85
## Character matrix gt cols: 10
## skip: 0
## nrows: 85
## row_num: 0
##
Processed variant: 85
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 49
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 102
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 102
## Character matrix gt cols: 10
## skip: 0
## nrows: 102
## row_num: 0
##
Processed variant: 102
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 99
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 99
## Character matrix gt cols: 10
## skip: 0
## nrows: 99
## row_num: 0
##
Processed variant: 99
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 53
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 53
## Character matrix gt cols: 10
## skip: 0
## nrows: 53
## row_num: 0
##
Processed variant: 53
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 86
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 86
## Character matrix gt cols: 10
## skip: 0
## nrows: 86
## row_num: 0
##
Processed variant: 86
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 105
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 105
## Character matrix gt cols: 10
## skip: 0
## nrows: 105
## row_num: 0
##
Processed variant: 105
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 51
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 89
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 89
## Character matrix gt cols: 10
## skip: 0
## nrows: 89
## row_num: 0
##
Processed variant: 89
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 39
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 39
## Character matrix gt cols: 10
## skip: 0
## nrows: 39
## row_num: 0
##
Processed variant: 39
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 88
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 88
## Character matrix gt cols: 10
## skip: 0
## nrows: 88
## row_num: 0
##
Processed variant: 88
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 49
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 71
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 71
## Character matrix gt cols: 10
## skip: 0
## nrows: 71
## row_num: 0
##
Processed variant: 71
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 77
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 77
## Character matrix gt cols: 10
## skip: 0
## nrows: 77
## row_num: 0
##
Processed variant: 77
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 65
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 65
## Character matrix gt cols: 10
## skip: 0
## nrows: 65
## row_num: 0
##
Processed variant: 65
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 17
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 17
## Character matrix gt cols: 10
## skip: 0
## nrows: 17
## row_num: 0
##
Processed variant: 17
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 127
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 127
## Character matrix gt cols: 10
## skip: 0
## nrows: 127
## row_num: 0
##
Processed variant: 127
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 51
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 130
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 130
## Character matrix gt cols: 10
## skip: 0
## nrows: 130
## row_num: 0
##
Processed variant: 130
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 30
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 30
## Character matrix gt cols: 10
## skip: 0
## nrows: 30
## row_num: 0
##
Processed variant: 30
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 93
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 93
## Character matrix gt cols: 10
## skip: 0
## nrows: 93
## row_num: 0
##
Processed variant: 93
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 31
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 31
## Character matrix gt cols: 10
## skip: 0
## nrows: 31
## row_num: 0
##
Processed variant: 31
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 69
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 69
## Character matrix gt cols: 10
## skip: 0
## nrows: 69
## row_num: 0
##
Processed variant: 69
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 11
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 11
## Character matrix gt cols: 10
## skip: 0
## nrows: 11
## row_num: 0
##
Processed variant: 11
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 43
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 85
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 85
## Character matrix gt cols: 10
## skip: 0
## nrows: 85
## row_num: 0
##
Processed variant: 85
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 46
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 107
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 107
## Character matrix gt cols: 10
## skip: 0
## nrows: 107
## row_num: 0
##
Processed variant: 107
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 48
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 49
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 32
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 32
## Character matrix gt cols: 10
## skip: 0
## nrows: 32
## row_num: 0
##
Processed variant: 32
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 43
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 25
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 25
## Character matrix gt cols: 10
## skip: 0
## nrows: 25
## row_num: 0
##
Processed variant: 25
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 46
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 103
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 103
## Character matrix gt cols: 10
## skip: 0
## nrows: 103
## row_num: 0
##
Processed variant: 103
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 46
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 110
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 110
## Character matrix gt cols: 10
## skip: 0
## nrows: 110
## row_num: 0
##
Processed variant: 110
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 42
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 22
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 22
## Character matrix gt cols: 10
## skip: 0
## nrows: 22
## row_num: 0
##
Processed variant: 22
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 30
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 30
## Character matrix gt cols: 10
## skip: 0
## nrows: 30
## row_num: 0
##
Processed variant: 30
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 22
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 22
## Character matrix gt cols: 10
## skip: 0
## nrows: 22
## row_num: 0
##
Processed variant: 22
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 25
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 25
## Character matrix gt cols: 10
## skip: 0
## nrows: 25
## row_num: 0
##
Processed variant: 25
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 19
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 19
## Character matrix gt cols: 10
## skip: 0
## nrows: 19
## row_num: 0
##
Processed variant: 19
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 39
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 39
## Character matrix gt cols: 10
## skip: 0
## nrows: 39
## row_num: 0
##
Processed variant: 39
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 97
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 97
## Character matrix gt cols: 10
## skip: 0
## nrows: 97
## row_num: 0
##
Processed variant: 97
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 42
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 80
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 80
## Character matrix gt cols: 10
## skip: 0
## nrows: 80
## row_num: 0
##
Processed variant: 80
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 20
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 20
## Character matrix gt cols: 10
## skip: 0
## nrows: 20
## row_num: 0
##
Processed variant: 20
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 1
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1
## Character matrix gt cols: 10
## skip: 0
## nrows: 1
## row_num: 0
##
Processed variant: 1
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## No snps for sample: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_freebayes_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 7
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 7
## Character matrix gt cols: 10
## skip: 0
## nrows: 7
## row_num: 0
##
Processed variant: 7
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 1
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1
## Character matrix gt cols: 10
## skip: 0
## nrows: 1
## row_num: 0
##
Processed variant: 1
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 8
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 8
## Character matrix gt cols: 10
## skip: 0
## nrows: 8
## row_num: 0
##
Processed variant: 8
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 3
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 3
## Character matrix gt cols: 10
## skip: 0
## nrows: 3
## row_num: 0
##
Processed variant: 3
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 35
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 35
## Character matrix gt cols: 10
## skip: 0
## nrows: 35
## row_num: 0
##
Processed variant: 35
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 105
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 105
## Character matrix gt cols: 10
## skip: 0
## nrows: 105
## row_num: 0
##
Processed variant: 105
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 38
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 126
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 126
## Character matrix gt cols: 10
## skip: 0
## nrows: 126
## row_num: 0
##
Processed variant: 126
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 17
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 17
## Character matrix gt cols: 10
## skip: 0
## nrows: 17
## row_num: 0
##
Processed variant: 17
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 15
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 15
## Character matrix gt cols: 10
## skip: 0
## nrows: 15
## row_num: 0
##
Processed variant: 15
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 22
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 22
## Character matrix gt cols: 10
## skip: 0
## nrows: 22
## row_num: 0
##
Processed variant: 22
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 15
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 15
## Character matrix gt cols: 10
## skip: 0
## nrows: 15
## row_num: 0
##
Processed variant: 15
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 31
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 31
## Character matrix gt cols: 10
## skip: 0
## nrows: 31
## row_num: 0
##
Processed variant: 31
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 14
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 14
## Character matrix gt cols: 10
## skip: 0
## nrows: 14
## row_num: 0
##
Processed variant: 14
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 50
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 68
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 68
## Character matrix gt cols: 10
## skip: 0
## nrows: 68
## row_num: 0
##
Processed variant: 68
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 51
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 51
## Character matrix gt cols: 10
## skip: 0
## nrows: 51
## row_num: 0
##
Processed variant: 51
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 74
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 74
## Character matrix gt cols: 10
## skip: 0
## nrows: 74
## row_num: 0
##
Processed variant: 74
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 38
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 3
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 3
## Character matrix gt cols: 10
## skip: 0
## nrows: 3
## row_num: 0
##
Processed variant: 3
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 17
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 17
## Character matrix gt cols: 10
## skip: 0
## nrows: 17
## row_num: 0
##
Processed variant: 17
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 0
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## No variant data: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_ivar_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 24
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 24
## Character matrix gt cols: 10
## skip: 0
## nrows: 24
## row_num: 0
##
Processed variant: 24
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 4
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 4
## Character matrix gt cols: 10
## skip: 0
## nrows: 4
## row_num: 0
##
Processed variant: 4
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 49
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 74
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 74
## Character matrix gt cols: 10
## skip: 0
## nrows: 74
## row_num: 0
##
Processed variant: 74
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 48
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 89
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 89
## Character matrix gt cols: 10
## skip: 0
## nrows: 89
## row_num: 0
##
Processed variant: 89
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 45
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 28
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 28
## Character matrix gt cols: 10
## skip: 0
## nrows: 28
## row_num: 0
##
Processed variant: 28
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 27
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 27
## Character matrix gt cols: 10
## skip: 0
## nrows: 27
## row_num: 0
##
Processed variant: 27
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 20
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 20
## Character matrix gt cols: 10
## skip: 0
## nrows: 20
## row_num: 0
##
Processed variant: 20
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 72
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 72
## Character matrix gt cols: 10
## skip: 0
## nrows: 72
## row_num: 0
##
Processed variant: 72
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 22
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 22
## Character matrix gt cols: 10
## skip: 0
## nrows: 22
## row_num: 0
##
Processed variant: 22
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 45
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 74
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 74
## Character matrix gt cols: 10
## skip: 0
## nrows: 74
## row_num: 0
##
Processed variant: 74
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 122
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 122
## Character matrix gt cols: 10
## skip: 0
## nrows: 122
## row_num: 0
##
Processed variant: 122
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 43
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 43
## Character matrix gt cols: 10
## skip: 0
## nrows: 43
## row_num: 0
##
Processed variant: 43
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 6
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 6
## Character matrix gt cols: 10
## skip: 0
## nrows: 6
## row_num: 0
##
Processed variant: 6
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 33
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 33
## Character matrix gt cols: 10
## skip: 0
## nrows: 33
## row_num: 0
##
Processed variant: 33
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 4
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 4
## Character matrix gt cols: 10
## skip: 0
## nrows: 4
## row_num: 0
##
Processed variant: 4
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 20
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 20
## Character matrix gt cols: 10
## skip: 0
## nrows: 20
## row_num: 0
##
Processed variant: 20
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 1
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1
## Character matrix gt cols: 10
## skip: 0
## nrows: 1
## row_num: 0
##
Processed variant: 1
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 47
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 70
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 70
## Character matrix gt cols: 10
## skip: 0
## nrows: 70
## row_num: 0
##
Processed variant: 70
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 47
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 81
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 81
## Character matrix gt cols: 10
## skip: 0
## nrows: 81
## row_num: 0
##
Processed variant: 81
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 44
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 52
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 52
## Character matrix gt cols: 10
## skip: 0
## nrows: 52
## row_num: 0
##
Processed variant: 52
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 76
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 76
## Character matrix gt cols: 10
## skip: 0
## nrows: 76
## row_num: 0
##
Processed variant: 76
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 54
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 54
## Character matrix gt cols: 10
## skip: 0
## nrows: 54
## row_num: 0
##
Processed variant: 54
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 59
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 59
## Character matrix gt cols: 10
## skip: 0
## nrows: 59
## row_num: 0
##
Processed variant: 59
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 46
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_freebayes_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 63
## header_line: 64
## variant count: 47
## column count: 10
##
Meta line 63 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element GL## Extracting gt element DP## Extracting gt element AD## Extracting gt element RO## Extracting gt element QR## Extracting gt element AO## Extracting gt element QA## Extracting gt element MIN_DP## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_hc_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 30
## header_line: 31
## variant count: 72
## column count: 10
##
Meta line 30 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 72
## Character matrix gt cols: 10
## skip: 0
## nrows: 72
## row_num: 0
##
Processed variant: 72
## All variants processed## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PL## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_ivar_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 7
## header_line: 8
## variant count: 49
## column count: 10
##
Meta line 7 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 10
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQ## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_mutect2_standard_unfiltered## Scanning file to determine attributes.
## File attributes:
## meta lines: 45
## header_line: 46
## variant count: 74
## column count: 10
##
Meta line 45 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 74
## Character matrix gt cols: 10
## skip: 0
## nrows: 74
## row_num: 0
##
Processed variant: 74
## All variants processed## Extracting gt element AD## Extracting gt element AF## Extracting gt element DP## Extracting gt element F1R2## Extracting gt element F2R1## Extracting gt element GQ## Extracting gt element GT## Extracting gt element PGT## Extracting gt element PID## Extracting gt element PL## Extracting gt element PS## Extracting gt element SB## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_timo_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 8
## header_line: 9
## variant count: 41
## column count: 10
##
Meta line 8 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 41
## Character matrix gt cols: 10
## skip: 0
## nrows: 41
## row_num: 0
##
Processed variant: 41
## All variants processed## Extracting gt element GT## Extracting gt element AD## Extracting gt element DP## Extracting gt element GQRun loferq data under standard setting
vcf_df_lofreq = arrange_no_gt_data( glue('{workdirectory}/lofreq/'), glue('{workdirectory}/lofreq/Reference_coding.fa'), annotated = 'no', ntlist=c('A','G','T','C'))## Number of chroms in fasta: 3## Length of input files: 97## Input vcf files include: c("/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_lofreq_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_lofreq_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//lofreq//000000000-K4LKV_l01_undetermined.fas_BWA_lofreq_standard.vcf")## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 496
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 496
## Character matrix gt cols: 8
## skip: 0
## nrows: 496
## row_num: 0
##
Processed variant: 496
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 511
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 511
## Character matrix gt cols: 8
## skip: 0
## nrows: 511
## row_num: 0
##
Processed variant: 511
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 0
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 8
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## No variant data: 000000000-K4LKV_l01_SynCon_Control03_rep1.fas_BWA_lofreq_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 4
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 4
## Character matrix gt cols: 8
## skip: 0
## nrows: 4
## row_num: 0
##
Processed variant: 4
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 48
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 8
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 0
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 8
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## No variant data: 000000000-K4LKV_l01_SynCon_Control06_rep1.fas_BWA_lofreq_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 3
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 3
## Character matrix gt cols: 8
## skip: 0
## nrows: 3
## row_num: 0
##
Processed variant: 3
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 0
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 8
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## No variant data: 000000000-K4LKV_l01_SynCon_Control08_rep1.fas_BWA_lofreq_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 89
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 89
## Character matrix gt cols: 8
## skip: 0
## nrows: 89
## row_num: 0
##
Processed variant: 89
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 79
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 79
## Character matrix gt cols: 8
## skip: 0
## nrows: 79
## row_num: 0
##
Processed variant: 79
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 97
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 97
## Character matrix gt cols: 8
## skip: 0
## nrows: 97
## row_num: 0
##
Processed variant: 97
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 65
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 65
## Character matrix gt cols: 8
## skip: 0
## nrows: 65
## row_num: 0
##
Processed variant: 65
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 71
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 71
## Character matrix gt cols: 8
## skip: 0
## nrows: 71
## row_num: 0
##
Processed variant: 71
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 90
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 90
## Character matrix gt cols: 8
## skip: 0
## nrows: 90
## row_num: 0
##
Processed variant: 90
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 91
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 91
## Character matrix gt cols: 8
## skip: 0
## nrows: 91
## row_num: 0
##
Processed variant: 91
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 62
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 62
## Character matrix gt cols: 8
## skip: 0
## nrows: 62
## row_num: 0
##
Processed variant: 62
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 88
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 88
## Character matrix gt cols: 8
## skip: 0
## nrows: 88
## row_num: 0
##
Processed variant: 88
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 68
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 68
## Character matrix gt cols: 8
## skip: 0
## nrows: 68
## row_num: 0
##
Processed variant: 68
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 152
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 152
## Character matrix gt cols: 8
## skip: 0
## nrows: 152
## row_num: 0
##
Processed variant: 152
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 63
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 63
## Character matrix gt cols: 8
## skip: 0
## nrows: 63
## row_num: 0
##
Processed variant: 63
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 73
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 8
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 67
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 67
## Character matrix gt cols: 8
## skip: 0
## nrows: 67
## row_num: 0
##
Processed variant: 67
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 58
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 58
## Character matrix gt cols: 8
## skip: 0
## nrows: 58
## row_num: 0
##
Processed variant: 58
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 73
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 8
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 59
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 59
## Character matrix gt cols: 8
## skip: 0
## nrows: 59
## row_num: 0
##
Processed variant: 59
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 56
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 56
## Character matrix gt cols: 8
## skip: 0
## nrows: 56
## row_num: 0
##
Processed variant: 56
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 62
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 62
## Character matrix gt cols: 8
## skip: 0
## nrows: 62
## row_num: 0
##
Processed variant: 62
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 60
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 60
## Character matrix gt cols: 8
## skip: 0
## nrows: 60
## row_num: 0
##
Processed variant: 60
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 68
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 68
## Character matrix gt cols: 8
## skip: 0
## nrows: 68
## row_num: 0
##
Processed variant: 68
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 69
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 69
## Character matrix gt cols: 8
## skip: 0
## nrows: 69
## row_num: 0
##
Processed variant: 69
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 80
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 80
## Character matrix gt cols: 8
## skip: 0
## nrows: 80
## row_num: 0
##
Processed variant: 80
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 68
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 68
## Character matrix gt cols: 8
## skip: 0
## nrows: 68
## row_num: 0
##
Processed variant: 68
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 64
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 8
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 55
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 55
## Character matrix gt cols: 8
## skip: 0
## nrows: 55
## row_num: 0
##
Processed variant: 55
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 69
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 69
## Character matrix gt cols: 8
## skip: 0
## nrows: 69
## row_num: 0
##
Processed variant: 69
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 78
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 78
## Character matrix gt cols: 8
## skip: 0
## nrows: 78
## row_num: 0
##
Processed variant: 78
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 65
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 65
## Character matrix gt cols: 8
## skip: 0
## nrows: 65
## row_num: 0
##
Processed variant: 65
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 66
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 66
## Character matrix gt cols: 8
## skip: 0
## nrows: 66
## row_num: 0
##
Processed variant: 66
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 50
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 8
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 78
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 78
## Character matrix gt cols: 8
## skip: 0
## nrows: 78
## row_num: 0
##
Processed variant: 78
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 63
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 63
## Character matrix gt cols: 8
## skip: 0
## nrows: 63
## row_num: 0
##
Processed variant: 63
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 108
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 108
## Character matrix gt cols: 8
## skip: 0
## nrows: 108
## row_num: 0
##
Processed variant: 108
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 66
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 66
## Character matrix gt cols: 8
## skip: 0
## nrows: 66
## row_num: 0
##
Processed variant: 66
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 86
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 86
## Character matrix gt cols: 8
## skip: 0
## nrows: 86
## row_num: 0
##
Processed variant: 86
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 49
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 49
## Character matrix gt cols: 8
## skip: 0
## nrows: 49
## row_num: 0
##
Processed variant: 49
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 71
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 71
## Character matrix gt cols: 8
## skip: 0
## nrows: 71
## row_num: 0
##
Processed variant: 71
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 50
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 8
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 134
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 134
## Character matrix gt cols: 8
## skip: 0
## nrows: 134
## row_num: 0
##
Processed variant: 134
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 72
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 72
## Character matrix gt cols: 8
## skip: 0
## nrows: 72
## row_num: 0
##
Processed variant: 72
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 66
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 66
## Character matrix gt cols: 8
## skip: 0
## nrows: 66
## row_num: 0
##
Processed variant: 66
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 82
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 82
## Character matrix gt cols: 8
## skip: 0
## nrows: 82
## row_num: 0
##
Processed variant: 82
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 91
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 91
## Character matrix gt cols: 8
## skip: 0
## nrows: 91
## row_num: 0
##
Processed variant: 91
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 56
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 56
## Character matrix gt cols: 8
## skip: 0
## nrows: 56
## row_num: 0
##
Processed variant: 56
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 89
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 89
## Character matrix gt cols: 8
## skip: 0
## nrows: 89
## row_num: 0
##
Processed variant: 89
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 78
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 78
## Character matrix gt cols: 8
## skip: 0
## nrows: 78
## row_num: 0
##
Processed variant: 78
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 138
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 138
## Character matrix gt cols: 8
## skip: 0
## nrows: 138
## row_num: 0
##
Processed variant: 138
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 116
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 116
## Character matrix gt cols: 8
## skip: 0
## nrows: 116
## row_num: 0
##
Processed variant: 116
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 64
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 8
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 190
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 190
## Character matrix gt cols: 8
## skip: 0
## nrows: 190
## row_num: 0
##
Processed variant: 190
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 64
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 8
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 126
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 126
## Character matrix gt cols: 8
## skip: 0
## nrows: 126
## row_num: 0
##
Processed variant: 126
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 64
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 8
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 194
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 194
## Character matrix gt cols: 8
## skip: 0
## nrows: 194
## row_num: 0
##
Processed variant: 194
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 63
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 63
## Character matrix gt cols: 8
## skip: 0
## nrows: 63
## row_num: 0
##
Processed variant: 63
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 88
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 88
## Character matrix gt cols: 8
## skip: 0
## nrows: 88
## row_num: 0
##
Processed variant: 88
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 57
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 57
## Character matrix gt cols: 8
## skip: 0
## nrows: 57
## row_num: 0
##
Processed variant: 57
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 80
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 80
## Character matrix gt cols: 8
## skip: 0
## nrows: 80
## row_num: 0
##
Processed variant: 80
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 116
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 116
## Character matrix gt cols: 8
## skip: 0
## nrows: 116
## row_num: 0
##
Processed variant: 116
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 64
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 64
## Character matrix gt cols: 8
## skip: 0
## nrows: 64
## row_num: 0
##
Processed variant: 64
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 83
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 83
## Character matrix gt cols: 8
## skip: 0
## nrows: 83
## row_num: 0
##
Processed variant: 83
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 194
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 194
## Character matrix gt cols: 8
## skip: 0
## nrows: 194
## row_num: 0
##
Processed variant: 194
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 139
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 139
## Character matrix gt cols: 8
## skip: 0
## nrows: 139
## row_num: 0
##
Processed variant: 139
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 101
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 101
## Character matrix gt cols: 8
## skip: 0
## nrows: 101
## row_num: 0
##
Processed variant: 101
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 67
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 67
## Character matrix gt cols: 8
## skip: 0
## nrows: 67
## row_num: 0
##
Processed variant: 67
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 83
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 83
## Character matrix gt cols: 8
## skip: 0
## nrows: 83
## row_num: 0
##
Processed variant: 83
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 94
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 94
## Character matrix gt cols: 8
## skip: 0
## nrows: 94
## row_num: 0
##
Processed variant: 94
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 82
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 82
## Character matrix gt cols: 8
## skip: 0
## nrows: 82
## row_num: 0
##
Processed variant: 82
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 67
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 67
## Character matrix gt cols: 8
## skip: 0
## nrows: 67
## row_num: 0
##
Processed variant: 67
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 121
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 121
## Character matrix gt cols: 8
## skip: 0
## nrows: 121
## row_num: 0
##
Processed variant: 121
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 72
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 72
## Character matrix gt cols: 8
## skip: 0
## nrows: 72
## row_num: 0
##
Processed variant: 72
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 98
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 98
## Character matrix gt cols: 8
## skip: 0
## nrows: 98
## row_num: 0
##
Processed variant: 98
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 39
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 39
## Character matrix gt cols: 8
## skip: 0
## nrows: 39
## row_num: 0
##
Processed variant: 39
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 105
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 105
## Character matrix gt cols: 8
## skip: 0
## nrows: 105
## row_num: 0
##
Processed variant: 105
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 35
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 35
## Character matrix gt cols: 8
## skip: 0
## nrows: 35
## row_num: 0
##
Processed variant: 35
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 87
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 87
## Character matrix gt cols: 8
## skip: 0
## nrows: 87
## row_num: 0
##
Processed variant: 87
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 9
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 9
## Character matrix gt cols: 8
## skip: 0
## nrows: 9
## row_num: 0
##
Processed variant: 9
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 108
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 108
## Character matrix gt cols: 8
## skip: 0
## nrows: 108
## row_num: 0
##
Processed variant: 108
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 33
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 33
## Character matrix gt cols: 8
## skip: 0
## nrows: 33
## row_num: 0
##
Processed variant: 33
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 81
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 81
## Character matrix gt cols: 8
## skip: 0
## nrows: 81
## row_num: 0
##
Processed variant: 81
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 12
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 12
## Character matrix gt cols: 8
## skip: 0
## nrows: 12
## row_num: 0
##
Processed variant: 12
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 82
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 82
## Character matrix gt cols: 8
## skip: 0
## nrows: 82
## row_num: 0
##
Processed variant: 82
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 37
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 8
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 75
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 75
## Character matrix gt cols: 8
## skip: 0
## nrows: 75
## row_num: 0
##
Processed variant: 75
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 6
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 6
## Character matrix gt cols: 8
## skip: 0
## nrows: 6
## row_num: 0
##
Processed variant: 6
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 67
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 67
## Character matrix gt cols: 8
## skip: 0
## nrows: 67
## row_num: 0
##
Processed variant: 67
## All variants processed## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 55
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 55
## Character matrix gt cols: 8
## skip: 0
## nrows: 55
## row_num: 0
##
Processed variant: 55
## All variants processed## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_lofreq_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 17
## header_line: 18
## variant count: 73
## column count: 8
##
Meta line 17 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 73
## Character matrix gt cols: 8
## skip: 0
## nrows: 73
## row_num: 0
##
Processed variant: 73
## All variants processed#Modify lofreq df for later rbind
vcf_df_lofreq = vcf_df_lofreq %>% add_column(REF_COUNT = NA) %>% add_column(ALT_COUNT = NA) %>% add_column(ChromKey = NA)
vcf_df_lofreq$AF = NULLRun varscan data under standard setting
vcf_df_var = arrange_gt_data_varscan( glue('{workdirectory}/varscan/'), glue('{workdirectory}/varscan/Reference_coding.fa'), annotated = 'no', ntlist=c('A','G','T','C'))## Number of chroms in fasta: 3## Length of input files: 94## Input vcf files include: c("/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_varscan_standard.vcf",
## "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_varscan_standard.vcf", "/Users/bessiewang/Desktop/GreshamLab/syntheticcontrols//varscan//000000000-K4LKV_l01_undetermined.fas_BWA_varscan_standard.vcf")## Sample name is: 000000000-K4LKV_l01_SynCon_Control01_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 140
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 140
## Character matrix gt cols: 10
## skip: 0
## nrows: 140
## row_num: 0
##
Processed variant: 140
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Control02_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 118
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 118
## Character matrix gt cols: 10
## skip: 0
## nrows: 118
## row_num: 0
##
Processed variant: 118
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 0
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## No variant data: 000000000-K4LKV_l01_SynCon_Control04_rep1.fas_BWA_varscan_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Control05_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 38
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 0
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## No variant data: 000000000-K4LKV_l01_SynCon_Control07_rep1.fas_BWA_varscan_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix01_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix02_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix03_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 36
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 36
## Character matrix gt cols: 10
## skip: 0
## nrows: 36
## row_num: 0
##
Processed variant: 36
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix04_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 30
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 30
## Character matrix gt cols: 10
## skip: 0
## nrows: 30
## row_num: 0
##
Processed variant: 30
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix05_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix06_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 39
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 39
## Character matrix gt cols: 10
## skip: 0
## nrows: 39
## row_num: 0
##
Processed variant: 39
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix07_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 29
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 29
## Character matrix gt cols: 10
## skip: 0
## nrows: 29
## row_num: 0
##
Processed variant: 29
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix08_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix09_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix10_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix11_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 38
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix12_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 24
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 24
## Character matrix gt cols: 10
## skip: 0
## nrows: 24
## row_num: 0
##
Processed variant: 24
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix13_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix14_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 37
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 10
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix15_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 24
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 24
## Character matrix gt cols: 10
## skip: 0
## nrows: 24
## row_num: 0
##
Processed variant: 24
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix16_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix17_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix18_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix19_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 41
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 41
## Character matrix gt cols: 10
## skip: 0
## nrows: 41
## row_num: 0
##
Processed variant: 41
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix20_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 30
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 30
## Character matrix gt cols: 10
## skip: 0
## nrows: 30
## row_num: 0
##
Processed variant: 30
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix21_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix22_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 48
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 37
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 10
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix23_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 28
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 28
## Character matrix gt cols: 10
## skip: 0
## nrows: 28
## row_num: 0
##
Processed variant: 28
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix24_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix25_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix26_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix27_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 37
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 37
## Character matrix gt cols: 10
## skip: 0
## nrows: 37
## row_num: 0
##
Processed variant: 37
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 50
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 50
## Character matrix gt cols: 10
## skip: 0
## nrows: 50
## row_num: 0
##
Processed variant: 50
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix28_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 26
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 26
## Character matrix gt cols: 10
## skip: 0
## nrows: 26
## row_num: 0
##
Processed variant: 26
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix29_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix30_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 42
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 42
## Character matrix gt cols: 10
## skip: 0
## nrows: 42
## row_num: 0
##
Processed variant: 42
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix31_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 34
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 34
## Character matrix gt cols: 10
## skip: 0
## nrows: 34
## row_num: 0
##
Processed variant: 34
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix32_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix33_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 48
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix34_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 48
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix35_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 38
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix36_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 26
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 26
## Character matrix gt cols: 10
## skip: 0
## nrows: 26
## row_num: 0
##
Processed variant: 26
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 44
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 44
## Character matrix gt cols: 10
## skip: 0
## nrows: 44
## row_num: 0
##
Processed variant: 44
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix37_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 30
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 30
## Character matrix gt cols: 10
## skip: 0
## nrows: 30
## row_num: 0
##
Processed variant: 30
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix38_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 19
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 19
## Character matrix gt cols: 10
## skip: 0
## nrows: 19
## row_num: 0
##
Processed variant: 19
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 38
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 38
## Character matrix gt cols: 10
## skip: 0
## nrows: 38
## row_num: 0
##
Processed variant: 38
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix39_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 1
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 1
## Character matrix gt cols: 10
## skip: 0
## nrows: 1
## row_num: 0
##
Processed variant: 1
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 32
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 32
## Character matrix gt cols: 10
## skip: 0
## nrows: 32
## row_num: 0
##
Processed variant: 32
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix40_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 15
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 15
## Character matrix gt cols: 10
## skip: 0
## nrows: 15
## row_num: 0
##
Processed variant: 15
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 0
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 0
## Character matrix gt cols: 10
## skip: 0
## nrows: 0
## row_num: 0
##
Processed variant: 0
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## No variant data: 000000000-K4LKV_l01_SynCon_Mix41_rep2.fas_BWA_varscan_standard## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 47
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 47
## Character matrix gt cols: 10
## skip: 0
## nrows: 47
## row_num: 0
##
Processed variant: 47
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix42_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 15
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 15
## Character matrix gt cols: 10
## skip: 0
## nrows: 15
## row_num: 0
##
Processed variant: 15
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix43_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 2
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 2
## Character matrix gt cols: 10
## skip: 0
## nrows: 2
## row_num: 0
##
Processed variant: 2
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep1.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 45
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 45
## Character matrix gt cols: 10
## skip: 0
## nrows: 45
## row_num: 0
##
Processed variant: 45
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_SynCon_Mix44_rep2.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 46
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 46
## Character matrix gt cols: 10
## skip: 0
## nrows: 46
## row_num: 0
##
Processed variant: 46
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADR## Sample name is: 000000000-K4LKV_l01_undetermined.fas_BWA_varscan_standard## Scanning file to determine attributes.
## File attributes:
## meta lines: 23
## header_line: 24
## variant count: 48
## column count: 10
##
Meta line 23 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 48
## Character matrix gt cols: 10
## skip: 0
## nrows: 48
## row_num: 0
##
Processed variant: 48
## All variants processed## Extracting gt element GT## Extracting gt element GQ## Extracting gt element SDP## Extracting gt element DP## Extracting gt element RD## Extracting gt element AD## Extracting gt element FREQ## Extracting gt element PVAL## Extracting gt element RBQ## Extracting gt element ABQ## Extracting gt element RDF## Extracting gt element RDR## Extracting gt element ADF## Extracting gt element ADRvcf_df_var = vcf_df_var %>% add_column(ChromKey = NA)#Merge df for all the callers
vcf_df = rbind(vcf_df, vcf_df_lofreq, vcf_df_var)Modify vcf_df for the later merging of vcf_df and the metadata
vcf_df$sample_name = vcf_df$sample
#print(head(vcf_df))
vcf_df = vcf_df %>% separate(sample_name, c("filename", "vcf_inputs"), sep='[.]')read in metadata
metadata = read.csv("Edited_metadata.csv", header = T)
#print(head(metadata))Merge the metadata with vcf_df
vcf_full = merge(vcf_df, metadata, by=c('filename'), all.x = T)
#print(head(vcf_full))#checking to make sure that the dimensions after merging are identical
dim(vcf_df)## [1] 37707 21dim(vcf_full)## [1] 37707 41#Dimensions are off by 10, checking the names of the files that are in the metadata but NOT included in our variant data
not_included = setdiff(levels(factor(vcf_full$filename)), levels(factor(vcf_df$filename)))
print(not_included)## character(0)#Check manually the metadata to confirm that we do not have variants in the above samples because they are WT and/or water controls
#Print off the names so they should all be wt control or empty
levels(factor((vcf_full %>% filter(filename %in% not_included))$SampleInfo))## character(0)#Re-merge to remove these files and check with Mohammed that 0 variants were found in these samples and weren't missed during analysis
vcf_full = merge(vcf_df, metadata, by=c('filename'), all.x = TRUE) # this will keep ALL variant data
#rechecking the dim - they should be identical now
dim(vcf_df)## [1] 37707 21dim(vcf_full)## [1] 37707 41#Modify vcf to remove files that are not used
message ("I'm removing samples that we are uncertain because of the metadata")## I'm removing samples that we are uncertain because of the metadatavcf_full = vcf_full %>% filter(Use == "yes") %>% unique() Merge vcf_full with SNV_info to select TP, FP, TN
SNVinfo = read.csv("SNV_info_allcaller.csv", header = T, check.names = FALSE)
#Right now the NA segment is treated as NA values in the df, so need to fix that
SNVinfo$CHROM = as.character(SNVinfo$CHROM)
SNVinfo$CHROM[is.na(SNVinfo$CHROM)] <- "NA"
#Right now the SNV_info is in wide format, change that into long format using pivot_longer
# we need the columns Copy_number and Expected_freq to be able to merge with your variant data, after merging na will appear in 'True' variables if it is a false-positive call!
SNVinfo = SNVinfo %>% pivot_longer(c("10000000", "1000000","100000","10000","1000"), names_to = "TrueExpectedCopyNumber", values_to = "Copy_number")
SNVinfo = SNVinfo %>% pivot_longer(c("0.5", "0.25", "0.125", '0.0625', '0.0313', '0.0156', '0.0078', '0.0039'), names_to = "TrueExpectedFrequency", values_to = "Expected_freq")
# Change the name of variant caller info
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_ivar_standard", "ivar")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_timo_standard", "timo")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_hc_standard", "hc")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_mutect2_standard_unfiltered", "mutect2")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_freebayes_standard", "freebayes")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_lofreq_standard", "lofreq")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_varscan_standard", "varscan")
#Merge SNVinfo with vcf_full
vcf_plus = merge(vcf_full, SNVinfo, by=c("POS","CHROM", "REF", "ALT", "Copy_number", "Expected_freq", "vcf_inputs"), all = TRUE)
#Replace NAs with 0
# use = 0 instead of = "0" so the following if_else can work (numeric values to use >, =, <)
vcf_plus$Expected_freq[is.na(vcf_plus$Expected_freq)] = 0
vcf_plus$ALT_FREQ[is.na(vcf_plus$ALT_FREQ)] = 0
vcf_plus$TrueExpectedCopyNumber[is.na(vcf_plus$TrueExpectedCopyNumber)] = 0
vcf_plus$TrueExpectedFrequency[is.na(vcf_plus$TrueExpectedFrequency)] = 0
#Using if.else to determine TP, FP, FN
vcf_plus = vcf_plus %>% mutate(type = ifelse( ALT_FREQ > 0 & TrueExpectedFrequency == 0, "FP",
ifelse(ALT_FREQ == 0 & TrueExpectedFrequency > 0, "FN",
ifelse(ALT_FREQ > 0 & TrueExpectedFrequency > 0, "TP", "NA"))))message("Remove 10^7 samples due to technical issues")## Remove 10^7 samples due to technical issuesvcf_plus = vcf_plus %>% filter(Copy_number != "10^7")What is the relationship between observed and expected allele frequency estimates? Fig 3C & Fig S6A
# Use only TPs - so we can answer the question: of the TP snps that we did find, how close were they to the expected freq?
TP = vcf_plus %>% filter (type == "TP", Rep == "rep1")
# Set colors for callers
tool_colors = c('#CC2F42', # freebayes - red
'#35B6E9', # hc - bright blue
'#009E73', # ivar - green
'#F9BECD', # lofreq - pink
'#F0E442', # mutect2 - yellow
'#CCD2EB', # timo - light purple
'#9B9E9A') # varscan, grey
tools = c("freebayes", "hc", "ivar", "lofreq", "mutect2", "timo", "varscan")
names(tool_colors) = tools
tool_colScale_fill <- scale_fill_manual(name = "Variant Caller",values = tool_colors)
tool_colScale <- scale_colour_manual(name = "Variant Caller",values = tool_colors)
TPmedian = TP %>% group_by(TrueExpectedFrequency, CHROM) %>% summarise(medianfreq = median(ALT_FREQ))## `summarise()` has grouped output by 'TrueExpectedFrequency'. You can override using the `.groups` argument.TP = merge(TP, TPmedian, by = c("TrueExpectedFrequency", "CHROM"))
# X-axis: True expected freq (FP should have an expected freq of 0)
# Order the grid so it would be PB2, HA, NA
TP$CHROM = factor(TP$CHROM, levels=c('PB2', 'HA', 'NA'))
Fig3A = ggplot(TP %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44")), aes(x = factor(round(medianfreq, digits = 3)), y = ALT_FREQ, color = vcf_inputs))+
labs(x="Median observed Frequency", y= "Observed Frequency") +
geom_point(width = 0.2, alpha = 0.3, position=position_dodge(width = 0.5)) +
tool_colScale+
facet_grid(.~CHROM, scales = "free", space = "free") +
theme_bw() +
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 13))+
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
stat_summary(fun = "median", geom = "point", col = "black",size = 2,shape = 18,fill = "red")## Warning: Ignoring unknown parameters: widthprint(Fig3A)
ggsave(Fig3A,
filename = glue("{workdirectory}/figures_new/Fig3A.png"),
width = 15,
height = 5, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(Fig3A,
filename = glue("{workdirectory}/figures_pdf_new/Fig3A.pdf"),
width = 15,
height = 5, limitsize=FALSE)#, useDingbats = FALSE)
# Set colors for copy numbers
cn_colors <- c( '#BBBBBB', '#999999',
'#777777',
'#555555',
'#333333')
copy_numbers = c("10^2", "10^3", "10^4", "10^5", "10^6")
names(cn_colors) = copy_numbers
cn_colScale_fill <- scale_fill_manual(name = "Copy Number",values = cn_colors)
cn_colScale <- scale_colour_manual(name = "Copy Number",values = cn_colors)
FigS6A = ggplot(TP, aes(x = as.numeric(Expected_freq), y = ALT_FREQ, color = Copy_number))+
labs(x="Expected Frequency", y= "Observed Frequency") +
geom_point(alpha = 0.8) +
facet_grid(CHROM~vcf_inputs) +
theme_bw() +
cn_colScale+
geom_abline(slope=1)+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 13))+
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS6A)
ggsave(FigS6A,
filename = glue("{workdirectory}/figures_new/FigS6A.png"),
width = 16,
height = 6.5, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS6A,
filename = glue("{workdirectory}/figures_pdf_new/FigS6A.pdf"),
width = 16,
height = 6.5, limitsize=FALSE)#, useDingbats = FALSE)Coverage plots - Fig S5C & S5D
# make a coverage plot for all samples across genome position
flu_covinfo = read.csv("cov_data.tsv", sep = "", header = T)
flu_covinfo = flu_covinfo %>% filter (name != "000000000-K4LKV_l01_undetermined.fas_BWA")
flu_covinfo$segment[is.na(flu_covinfo$segment)] <- "NA"
flu_cov = separate(flu_covinfo,name,sep = "_",
into = c("IDK", "IDKk", "IDkkk", "Sample", "Rep")) %>%
select(!c("IDK","IDKk","IDkkk"))## Warning: Expected 5 pieces. Additional pieces discarded in 495972 rows [1, 2, 3,
## 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].flu_cov$Rep<-gsub(".fas","",as.character(flu_cov$Rep))
flu_cov = flu_cov %>% filter(Sample != "Control01") %>% filter(Sample != "Control02")%>% filter(Sample != "Control04")%>% filter(Sample != "Control05")
# Set gradient colors for all samples
sample_colors = c("#373737", "#323232", "#2D2D2D","#282828", "#232323","#1E1E1E", "#191919", "#141414", "#0F0F0F", "#0A0A0A","#3C3C3C","#414141", "#464646", "#4B4B4B", "#505050", "#555555", "#5A5A5A", "#5F5F5F", "#646464", "#696969","#6E6E6E","#737373", "#787878", "#7D7D7D", "#828282", "#878787","#8C8C8C", "#919191", "#969696", "#9B9B9B", "#ADADAD","#A5A5A5", "#AAAAAA", "#AFAFAF", "#B4B4B4", "#B9B9B9", "#BEBEBE", "#C3C3C3","#C8C8C8", "#CDCDCD", "#D2D2D2", "#D7D7D7", "#DCDCDC", "#E1E1E1")
samples = c("Mix01", "Mix02", "Mix03", "Mix04", "Mix05", "Mix06", "Mix07", "Mix08", "Mix09", "Mix10", "Mix11","Mix12", "Mix13", "Mix14", "Mix15", "Mix16", "Mix17", "Mix18", "Mix19", "Mix20", "Mix21", "Mix22", "Mix23", "Mix24", "Mix25", "Mix26", "Mix27", "Mix28", "Mix29", "Mix30", "Mix31", "Mix32", "Mix33", "Mix34", "Mix35", "Mix36", "Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix43", "Mix44")
names(sample_colors) = samples
sample_colScale_fill <- scale_fill_manual(name = "Samples",values = sample_colors)
sample_colScale <- scale_colour_manual(name = "Samples",values = sample_colors)
flu_cov$segment = factor(flu_cov$segment, levels=c("PB2", "HA", "NA"))
FigS5C = ggplot(data = flu_cov, aes(x=ntpos, y=log10(totalcount), color = Sample)) +
geom_line(aes(group=Sample), size = 1) +
theme_bw() +
sample_colScale+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +
facet_grid(Rep~segment, scales = "free_x") +
xlab("Nucleotide Position") +
ylab("Log10 Read Depth")
print(FigS5C)
ggsave(FigS5C,
filename = glue("{workdirectory}/FigS5C.png"),
width = 12,
height = 7, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS5C,
filename = glue("{workdirectory}/figures_pdf/FigS5C.pdf"),
width = 12,
height = 7, limitsize=FALSE)#, useDingbats = FALSE)
## what are the bad samples? need to exclude them from the analysis
bad_samples = flu_cov %>% filter (log10(totalcount) < 2)
unique(bad_samples$Sample)## [1] "Mix37" "Mix38" "Mix39" "Mix40" "Mix41" "Mix42" "Mix44"flu_cov = flu_cov %>% filter(!Sample %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))
##calculate the average coverage for each sample. then plot: X-axis: sample, y-axis:avg coverage, geom_point
cov_avg = flu_cov %>% group_by(Sample, segment, Rep) %>% summarise(sample_avg_cov = mean(totalcount))## `summarise()` has grouped output by 'Sample', 'segment'. You can override using the `.groups` argument.# Set color for replicates
rep12_colors = c('#2F142B', # rep1
'#43668B')# rep2
rep12names = c("rep1", "rep2")
names(rep12_colors) = rep12names
rep12_colScale_fill <- scale_fill_manual(name = "Rep",values = rep12_colors)
rep12_colScale <- scale_colour_manual(name = "Rep",values = rep12_colors)
FigS5D = ggplot(cov_avg, aes(x = Sample, y = log10(sample_avg_cov), color = Rep))+
labs(x="Sample", y= "Log10(Average Coverage)") +
geom_point(alpha = 0.8) +
facet_grid(.~segment,scales = "free") +
rep12_colScale+
theme_bw() +
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS5D)
ggsave(FigS5D,
filename = glue("{workdirectory}/FigS5D.png"),
width = 12,
height = 5, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS5D,
filename = glue("{workdirectory}/figures_pdf/FigS5D.pdf"),
width = 12,
height = 5, limitsize=FALSE)#, useDingbats = FALSE)Create the replicate df
# separate rep1 from rep2
rep1 = vcf_plus %>% filter(Rep == "rep1") %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))
rep2 = vcf_plus %>% filter(Rep == "rep2") %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))
# merge the replicates
replicates = merge(rep1, rep2,
by.x =c('CHROM', "Copy_number", "POS", "Expected_freq", "REF", "ALT", "ChromKey", "vcf_inputs", "Use", "Cohort", "repname"),
by.y = c('CHROM', "Copy_number", "POS", "Expected_freq", "REF", "ALT", "ChromKey", "vcf_inputs", "Use", "Cohort", "Sample"), all = T)
#Change NA to zero
replicates$ALT_FREQ.x[is.na(replicates$ALT_FREQ.x)] = 0
replicates$ALT_FREQ.y[is.na(replicates$ALT_FREQ.y)] = 0
replicates$type.x[is.na(replicates$type.x)] = "NONE"
replicates$type.y[is.na(replicates$type.y)] = "NONE"
# Remove the controls for this analysis
replicates = replicates %>% filter(!Copy_number == "control")
# specify the four categories
replicates = replicates %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == "TP" & type.y != "TP", "rep1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'rep2_tp',
ifelse(type.x == 'FP' & type.y != 'FP' | type.x != 'FP' & type.y == 'FP', 'single_fp', "NA"))))))How we find the transcription errors - Fig S5E
replicates$VAR = paste0(replicates$CHROM, '_', replicates$POS,'_', replicates$ALT)
#replicates %>% filter(Category == "both_fp")
reduced_reps_df = replicates %>% filter(Category == "both_fp") %>%
select(CHROM, POS, ALT,ALT_FREQ.y,VAR, ALT_FREQ.x, REF, Category, Expected_freq, Copy_number, vcf_inputs) %>%
unique()
reduced_reps_df = reduced_reps_df %>% group_by(Expected_freq, CHROM, POS, ALT, VAR,vcf_inputs) %>%
add_tally(name = 'copy_number_count') %>%
unique() %>% ungroup() %>% group_by(Copy_number, CHROM, POS, ALT, VAR,vcf_inputs) %>%
add_tally(name = 'Expected_freq_count') %>% ungroup() %>%
group_by(Copy_number, CHROM, POS, ALT, VAR, Expected_freq) %>%
add_tally(name = 'vcf_type_count') %>% ungroup()
# Filter for transcription errors
transcription_err = levels(factor((reduced_reps_df %>% filter(copy_number_count >1 &
Expected_freq_count > 1 &
vcf_type_count >=2 &
vcf_inputs %in% c("varscan","ivar","timo","freebayes")) %>% unique())$VAR))
transcription_errors = reduced_reps_df %>% filter(VAR %in% transcription_err)
transcription_errors$error_type = "pre_MRTPCR"
other_errors = reduced_reps_df %>% filter(!VAR %in% levels(factor(transcription_errors$VAR)))
other_errors$error_type = "post_MRTPCR"
error_df= rbind(transcription_errors, other_errors)
error_df$CHROM = factor(error_df$CHROM, levels = c("PB2", "HA", "NA"))
error_df$vcf_inputs = factor(error_df$vcf_inputs, levels = c("lofreq","hc","mutect2","freebayes","timo", "ivar","varscan"))
# Set color for nucleotides
nt_colors = c('#d7191c', # red - A
'#abd9e9', # light blue - T
'#fdae61', # orange - C
'#2c7bb6') # dark blue - G
nt = c("A", "T", "C", "G")
names(nt_colors) = nt
nt_colScale_fill <- scale_fill_manual(name = "Nucleotide",values = nt_colors)
nt_colScale <- scale_colour_manual(name = "Nucleotide",values = nt_colors)
FigS5E = ggplot(error_df, aes(x=VAR, y=vcf_inputs,fill = ALT)) +
geom_tile(alpha = 0.8) +
facet_grid(error_type~CHROM, scales = 'free')+
nt_colScale_fill+
theme(axis.text.x=element_blank(), #remove x axis labels
axis.ticks.x=element_blank(),
legend.key = element_blank(),
strip.background = element_rect(colour= "black", fill= "white"))
print(FigS5E)
ggsave(FigS5E,
filename = glue("{workdirectory}/figures_new/FigS5E.png"),
width = 10,
height = 5, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS5E,
filename = glue("{workdirectory}/figures_pdf_new/FigS5E.pdf"),
width = 10,
height = 5, limitsize=FALSE)#, useDingbats = FALSE)what’s the relationship between allele freq estimates between replicates? - Figure S7A
## Change the category of transcription errors we found into "transcription error"
Transcription_error = replicates %>% filter(CHROM %in% c("PB2", "HA", "NA"), POS %in% c("596", "114", "176", "2102", "2197", "2207", "1367"), ALT %in% c("A" , "G")) %>% filter(Category == "both_fp") %>% mutate(Category = replace(Category, Category == "both_fp", "pre_MRTPCR"))
replicates = replicates %>% filter (!(CHROM == "HA"& POS == "596"& ALT == "A" & Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "114"& ALT == "A"& Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "176"& ALT == "A"& Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "2102"& ALT == "G"& Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "2197"& ALT == "G"& Category == "both_fp")) %>% filter (!(CHROM == "PB2"& POS == "2207"& ALT == "G"& Category == "both_fp")) %>% filter (!(CHROM == "NA"& POS == "1367"& ALT == "A"& Category == "both_fp"))
replicates = rbind(replicates, Transcription_error)
#Set colors for categories
category_colors = c('#2F142B', # both TP
'#E86F3F', # both FP
'#5E2A59', # one rep TP
'#5E2A59', # one rep TP
'#F2A07B',# one rep FP
"#F0E442")#preMRTPCR
categories = c('both_tp','both_fp','rep1_tp','rep2_tp','single_fp', 'pre_MRTPCR' )
names(category_colors) = categories
category_colScale_fill <- scale_fill_manual(name = "Category",values = category_colors)
category_colScale <- scale_colour_manual(name = "Category",values = category_colors)
#Plot: observed freq in rep1 against observed freq in rep2
#Create layers so that the both_fp category are on the toppest layer of the graph for better visualization (otherwise it will be blocked by both_tp becuse there are a lot of them)
FPlayer = replicates %>% filter(Category == "both_fp")
Othertype = replicates %>% filter(!Category == "both_fp")
## Annotate the percentage of TP & FPs shared between two replicates for each caller
ivar_both_fp = replicates %>% filter(Category == "both_fp", vcf_inputs =="ivar")
ivar_both_tp = replicates %>% filter(Category == "both_tp", vcf_inputs =="ivar")
hc_both_fp = replicates %>% filter(Category == "both_fp", vcf_inputs =="hc")
hc_both_tp = replicates %>% filter(Category == "both_tp", vcf_inputs =="hc")
timo_both_fp = replicates %>% filter(Category == "both_fp", vcf_inputs =="timo")
timo_both_tp = replicates %>% filter(Category == "both_tp", vcf_inputs =="timo")
mutect2_both_fp = replicates %>% filter(Category == "both_fp", vcf_inputs =="mutect2")
mutect2_both_tp = replicates %>% filter(Category == "both_tp", vcf_inputs =="mutect2")
lofreq_both_fp = replicates %>% filter(Category == "both_fp", vcf_inputs =="lofreq")
lofreq_both_tp = replicates %>% filter(Category == "both_tp", vcf_inputs =="lofreq")
varscan_both_fp = replicates %>% filter(Category == "both_fp", vcf_inputs =="varscan")
varscan_both_tp = replicates %>% filter(Category == "both_tp", vcf_inputs =="varscan")
freebayes_both_fp = replicates %>% filter(Category == "both_fp", vcf_inputs =="freebayes")
freebayes_both_tp = replicates %>% filter(Category == "both_tp", vcf_inputs =="freebayes")
## Create an additional data frame to hold the text annotations
Annotation_fp = data.frame(
label = c( "0.18%","1.7%","0%","2.7%","10.4%","19.6%","22.3%"),
vcf_inputs_f = c( "varscan", "ivar","timo","freebayes", "mutect2", "hc", "lofreq"))
FPlayer$vcf_inputs_f = factor(FPlayer$vcf_inputs, levels=c("varscan", "ivar","timo","freebayes", "mutect2", "hc", "lofreq"))
Othertype$vcf_inputs_f = factor(Othertype$vcf_inputs, levels=c("varscan", "ivar","timo","freebayes", "mutect2", "hc", "lofreq"))
# Zoom in the figure, looking at observed frequency less or equal to 0.25
Othertype_v2 = Othertype %>% filter(ALT_FREQ.x <= 0.25, ALT_FREQ.y <=0.25)
FPlayer_v2 = FPlayer %>% filter(ALT_FREQ.x <= 0.25, ALT_FREQ.y <=0.25)
FigS7A = ggplot() +
geom_point(data= Othertype_v2, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
geom_point(data=FPlayer_v2, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
labs(x="Observed Frequency Rep1", y= "Observed Frequency Rep2") +
category_colScale +
theme_bw() +
facet_grid(.~vcf_inputs_f) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))+
annotate(geom = "segment", x = 0.1, y = 0.025, xend = 0.025, yend = 0.015, curvature = .3, arrow = arrow(length = unit(1, "mm"))) +
geom_text(x = 0.13, y = 0.028, aes(label = label), data = Annotation_fp, size = 3)## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: width## Warning: Ignoring unknown parameters: curvatureprint(FigS7A)
ggsave(FigS7A,
filename = glue("{workdirectory}/figures_new/FigS7A.png"),
width = 15,
height = 3, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS7A,
filename = glue("{workdirectory}/figures_pdf_new/FigS7A.pdf"),
width = 15,
height = 3, limitsize=FALSE)#, useDingbats = FALSE)SNV map: showing both engineered SNVs and in-vitro transcription errors - FigureS5A
SNVTransErr = read.csv("Transcription_error_binom.csv", header = T, check.names = FALSE)
SNVTransErr$CHROM = as.character(SNVTransErr$CHROM)
SNVTransErr$CHROM[is.na(SNVTransErr$CHROM)] <- "NA"
SNVinfo$CHROM[is.na(SNVinfo$CHROM)] <- "NA"
SNVinfo$CHROM = factor(SNVinfo$CHROM, levels=c('PB2', 'HA', 'NA'))
SNVTransErr$CHROM = factor(SNVTransErr$CHROM, levels=c('PB2', 'HA', 'NA'))
FigS5A = ggplot() +
geom_segment(data = SNVinfo, aes(x = POS, xend = POS, y=0, yend = 1),alpha = 0.8, color = "azure4") +
geom_segment(data = SNVTransErr, aes(x = POS, xend = POS, y=0, yend = 1, linetype= "Pre-MRTPCR error"),alpha = 0.8, color = "red") +
facet_grid(.~CHROM, scales = "free_x", space = 'free_x') +
ylab("") +
xlab("Genome position") +
scale_x_continuous(expand = c(0, 0))+
theme(panel.background = element_blank(),
axis.line = element_line(colour = "gray"),
legend.key = element_blank(),
strip.background = element_rect(colour="gray", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
panel.border = element_rect(colour='gray', fill = NA),
axis.ticks.y = element_blank(),
axis.text.y = element_blank(), legend.position="bottom",
legend.title=element_blank())
print(FigS5A)
ggsave(FigS5A,
filename = glue("{workdirectory}/Figures/FigS5A.png"),
width = 17,
height = 2, limitsize=FALSE)#, useDingbats = FALSE)
ggsave(FigS5A,
filename = glue("{workdirectory}/figures_pdf/FigS5A.pdf"),
width = 17,
height = 2, limitsize=FALSE)#, useDingbats = FALSE)
# SNV map without transcription error
SNVmap_noTE = ggplot() +
geom_segment(data = SNVinfo, aes(x = POS, xend = POS, y=0, yend = 1),alpha = 1, color = "azure4", size = 1) +
#geom_segment(data = SNVTransErr, aes(x = POS, xend = POS, y=0, yend = 1, linetype= "Pre-MRTPCR error"),alpha = 0.8, color = "red") +
facet_grid(.~CHROM, scales = "free_x", space = 'free_x') +
ylab("") +
xlab("Genome position") +
scale_x_continuous(expand = c(0, 0))+
theme(panel.background = element_blank(),
axis.line = element_line(colour = "gray"),
legend.key = element_blank(),
strip.background = element_rect(colour="gray", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
panel.border = element_rect(colour='gray', fill = NA),
axis.ticks.y = element_blank(),
axis.text.y = element_blank(), legend.position="bottom",
legend.title=element_blank())
print(SNVmap_noTE)
ggsave(SNVmap_noTE,
filename = glue("{workdirectory}/Figures/SNVmap_noTE.png"),
width = 17,
height = 2, limitsize=FALSE)#, useDingbats = FALSE)So right now, create a new SNV_info that include the transcription error positions, the rest of the analysis should be based on this SNV_info
SNVinfo = read.csv("SNV_info_with_transcriptionerror_binom.csv", header = T, check.names = FALSE)
#Right now the NA segment is treated as NA values in the df, so need to fix that
SNVinfo$CHROM = as.character(SNVinfo$CHROM)
SNVinfo$CHROM[is.na(SNVinfo$CHROM)] <- "NA"
#Right now the SNV_info is in wide format, change that into long format using pivot_longer
# we need the columns Copy_number and Expected_freq to be able to merge with your variant data, after merging na will appear in 'True' variables if it is a false-positive call!
SNVinfo = SNVinfo %>% pivot_longer(c("10000000", "1000000","100000","10000","1000"), names_to = "TrueExpectedCopyNumber", values_to = "Copy_number")
SNVinfo = SNVinfo %>% pivot_longer(c("0.5", "0.25", "0.125", '0.0625', '0.0313', '0.0156', '0.0078', '0.0039'), names_to = "TrueExpectedFrequency", values_to = "Expected_freq")
# Change the name of variant caller info
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_ivar_standard", "ivar")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_timo_standard", "timo")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_hc_standard", "hc")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_mutect2_standard_unfiltered", "mutect2")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_freebayes_standard", "freebayes")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_lofreq_standard", "lofreq")
vcf_full$vcf_inputs <- replace(vcf_full$vcf_inputs, vcf_full$vcf_inputs=="fas_BWA_varscan_standard", "varscan")
#Merge SNVinfo with vcf_full
vcf_plus = merge(vcf_full, SNVinfo, by=c("POS","CHROM", "REF", "ALT", "Copy_number", "Expected_freq", "vcf_inputs", "Rep"), all = TRUE)
#Replace NAs with 0
# use = 0 instead of = "0" so the following if_else can work (numeric values to use >, =, <)
vcf_plus$Expected_freq[is.na(vcf_plus$Expected_freq)] = 0
vcf_plus$ALT_FREQ[is.na(vcf_plus$ALT_FREQ)] = 0
vcf_plus$TrueExpectedCopyNumber[is.na(vcf_plus$TrueExpectedCopyNumber)] = 0
vcf_plus$TrueExpectedFrequency[is.na(vcf_plus$TrueExpectedFrequency)] = 0
#test831 = vcf_plus %>% filter(POS == "831" & CHROM == "HA")
#Using if.else to determine TP, FP, FN
vcf_plus = vcf_plus %>% mutate(type = ifelse( ALT_FREQ > 0 & TrueExpectedFrequency == 0, "FP",
ifelse(ALT_FREQ == 0 & TrueExpectedFrequency > 0, "FN",
ifelse(ALT_FREQ > 0 & TrueExpectedFrequency > 0, "TP", "NA"))))
vcf_plus = vcf_plus %>% filter(Copy_number != "10^7") How well the variant callers agreed on the frequency of the variants predicted? - FigureS6B Note: Need to combine all these figures to make the whole S6B
#plot the frequency of a variant in one caller against the frequency in each of the other callers
Timofreq = vcf_plus %>% filter(vcf_inputs == "timo", Rep == "rep1")
hcfreq = vcf_plus %>% filter(vcf_inputs == "hc", Rep == "rep1")
ivarfreq = vcf_plus %>% filter(vcf_inputs == "ivar", Rep == "rep1")
freebayesfreq = vcf_plus %>% filter(vcf_inputs == "freebayes", Rep == "rep1")
varscanfreq = vcf_plus %>% filter(vcf_inputs == "varscan", Rep == "rep1")
# Timo vs Haplotypecaller
timohc = merge(Timofreq, hcfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
timohc = timohc%>%filter(!Copy_number == "control")
timohc$type.x[is.na(timohc$type.x)] <- "NA"
timohc$type.y[is.na(timohc$type.y)] <- "NA"
timohc = timohc %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#Set colors
category_colors_1 = c( '#E86F3F', '#2F142B','#5E2A59','#5E2A59', '#F2A07B','#43668B', '#43668B')
categories_1 = c('both_fp','both_tp','caller1_tp','caller2_tp', "single_fp", "single_fn", "both_fn")
names(category_colors_1) = categories_1
category_colScale_fill_1 <- scale_fill_manual(name = "Category",values = category_colors_1)
category_colScale_1 <- scale_colour_manual(name = "Category",values = category_colors_1)
#calculate both TP%
timohc_bothtp = timohc %>% filter(Category == "both_tp")
#calculate both FP%
timohc_counts = timohc %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
timohc_counts$both_tp[is.na(timohc_counts$both_tp)] = 0
#timohc_counts$both_fp[is.na(timohc_counts$both_fp)] = 0
timohc_counts$both_fn[is.na(timohc_counts$both_fn)] = 0
sum(timohc_counts$both_fp)/(sum(timohc_counts$both_fp)+sum(timohc_counts$both_tp))## Warning: Unknown or uninitialised column: `both_fp`.
## Warning: Unknown or uninitialised column: `both_fp`.## [1] 0Figtimohc = ggplot(timohc, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category)) +
labs(x="timo", y= "hc") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 61.6%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0%", hjust = "left")## Warning: Ignoring unknown parameters: width #facet_grid(.~Copy_number)
print(Figtimohc)## Warning: Removed 1535 rows containing missing values (geom_point).
ggsave(Figtimohc,
filename = glue("{workdirectory}/figures_new/Figtimohc.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 1535 rows containing missing values (geom_point).ggsave(Figtimohc,
filename = glue("{workdirectory}/figures_pdf/Figtimohc.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 1535 rows containing missing values (geom_point).#timo vs ivar
timoivar = merge(Timofreq, ivarfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
timoivar = timoivar%>%filter(!Copy_number == "control")
timoivar$type.x[is.na(timoivar$type.x)] <- "NA"
timoivar$type.y[is.na(timoivar$type.y)] <- "NA"
timoivar = timoivar %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
timoivar_bothtp = timoivar %>% filter(Category == "both_tp")
#calculate both FP%
timoivar_counts = timoivar %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
timoivar_counts$both_tp[is.na(timoivar_counts$both_tp)] = 0
timoivar_counts$both_fp[is.na(timoivar_counts$both_fp)] = 0
timoivar_counts$both_fn[is.na(timoivar_counts$both_fn)] = 0
sum(timoivar_counts$both_fp)/(sum(timoivar_counts$both_fp)+sum(timoivar_counts$both_tp))## [1] 0.0008710801FPlayer_timoivar = timoivar %>% filter(Category == "both_fp")
Othertype_timoivar = timoivar %>% filter(!Category == "both_fp")
Figtimoivar = ggplot() +
geom_point(data= Othertype_timoivar, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
geom_point(data=FPlayer_timoivar, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
labs(x="timo", y= "ivar") +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 70.3%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0.09%", hjust = "left")## Warning: Ignoring unknown parameters: width## Warning: Ignoring unknown parameters: widthprint(Figtimoivar)## Warning: Removed 56 rows containing missing values (geom_point).
ggsave(Figtimoivar,
filename = glue("{workdirectory}/figures_new/Figtimoivar.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 56 rows containing missing values (geom_point).ggsave(Figtimoivar,
filename = glue("{workdirectory}/figures_pdf/Figtimoivar.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 56 rows containing missing values (geom_point).#timo vs freebayes
timofb = merge(Timofreq, freebayesfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
timofb = timofb%>%filter(!Copy_number == "control")
timofb$type.x[is.na(timofb$type.x)] <- "NA"
timofb$type.y[is.na(timofb$type.y)] <- "NA"
timofb = timofb %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
timofb_bothtp = timofb %>% filter(Category == "both_tp")
#calculate both FP%
timofb_counts = timofb %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
timofb_counts$both_tp[is.na(timofb_counts$both_tp)] = 0
timofb_counts$both_fp[is.na(timofb_counts$both_fp)] = 0
timofb_counts$both_fn[is.na(timofb_counts$both_fn)] = 0
sum(timofb_counts$both_fp)/(sum(timofb_counts$both_fp)+sum(timofb_counts$both_tp))## [1] 0.001034126FPlayer_timofb = timofb %>% filter(Category == "both_fp")
Othertype_timofb = timofb %>% filter(!Category == "both_fp")
Figtimofb = ggplot() +
geom_point(data= Othertype_timofb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
geom_point(data=FPlayer_timofb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
labs(x="timo", y= "freebayes") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 59.2%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0.10%", hjust = "left")## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: widthprint(Figtimofb)## Warning: Removed 97 rows containing missing values (geom_point).
ggsave(Figtimofb,
filename = glue("{workdirectory}/figures_new/Figtimofb.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 97 rows containing missing values (geom_point).ggsave(Figtimofb,
filename = glue("{workdirectory}/figures_pdf/Figtimofb.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 97 rows containing missing values (geom_point).#timo vs varscan
timovarscan = merge(Timofreq, varscanfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
timovarscan = timovarscan%>%filter(!Copy_number == "control")
timovarscan$type.x[is.na(timovarscan$type.x)] <- "NA"
timovarscan$type.y[is.na(timovarscan$type.y)] <- "NA"
timovarscan = timovarscan %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
timovarscan_bothtp = timovarscan %>% filter(Category == "both_tp")
#calculate both FP%
timovarscan_counts = timovarscan %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
timovarscan_counts$both_tp[is.na(timovarscan_counts$both_tp)] = 0
timovarscan_counts$both_fp[is.na(timovarscan_counts$both_fp)] = 0
timovarscan_counts$both_fn[is.na(timovarscan_counts$both_fn)] = 0
sum(timovarscan_counts$both_fp)/(sum(timovarscan_counts$both_fp)+sum(timovarscan_counts$both_tp))## [1] 0.0008733624FPlayer_timovarscan = timovarscan %>% filter(Category == "both_fp")
Othertype_timovarscan = timovarscan %>% filter(!Category == "both_fp")
Figtimovarscan = ggplot() +
geom_point(data= Othertype_timovarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
geom_point(data=FPlayer_timovarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
labs(x="timo", y= "varscan") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 70.1%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0.09%", hjust = "left")## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: widthprint(Figtimovarscan)## Warning: Removed 15 rows containing missing values (geom_point).
ggsave(Figtimovarscan,
filename = glue("{workdirectory}/figures_new/Figtimovarscan.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 15 rows containing missing values (geom_point).ggsave(Figtimovarscan,
filename = glue("{workdirectory}/figures_pdf/Figtimovarscan.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 15 rows containing missing values (geom_point).#ivar vs hc
ivarhc = merge(ivarfreq, hcfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
ivarhc = ivarhc%>%filter(!Copy_number == "control")
ivarhc$type.x[is.na(ivarhc$type.x)] <- "NA"
ivarhc$type.y[is.na(ivarhc$type.y)] <- "NA"
ivarhc = ivarhc %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
ivarhc_bothtp = ivarhc %>% filter(Category == "both_tp")
#calculate both FP%
ivarhc_counts = ivarhc %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
ivarhc_counts$both_tp[is.na(ivarhc_counts$both_tp)] = 0
ivarhc_counts$both_fp[is.na(ivarhc_counts$both_fp)] = 0
ivarhc_counts$both_fn[is.na(ivarhc_counts$both_fn)] = 0
sum(ivarhc_counts$both_fp)/(sum(ivarhc_counts$both_fp)+sum(ivarhc_counts$both_tp))## [1] 0.01701783Figivarhc = ggplot(ivarhc, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category)) +
labs(x="ivar", y= "hc") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 74.3%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 1.7%", hjust = "left")## Warning: Ignoring unknown parameters: widthprint(Figivarhc)## Warning: Removed 1549 rows containing missing values (geom_point).
ggsave(Figivarhc,
filename = glue("{workdirectory}/figures_new/Figivarhc.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 1549 rows containing missing values (geom_point).ggsave(Figivarhc,
filename = glue("{workdirectory}/figures_pdf/Figivarhc.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 1549 rows containing missing values (geom_point).#ivar vs fb
ivarfb = merge(ivarfreq, freebayesfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
ivarfb = ivarfb%>%filter(!Copy_number == "control")
ivarfb$type.x[is.na(ivarfb$type.x)] <- "NA"
ivarfb$type.y[is.na(ivarfb$type.y)] <- "NA"
ivarfb = ivarfb %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
ivarfb_bothtp = ivarfb %>% filter(Category == "both_tp")
#calculate both FP%
ivarfb_counts = ivarfb %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
ivarfb_counts$both_tp[is.na(ivarfb_counts$both_tp)] = 0
ivarfb_counts$both_fp[is.na(ivarfb_counts$both_fp)] = 0
ivarfb_counts$both_fn[is.na(ivarfb_counts$both_fn)] = 0
sum(ivarfb_counts$both_fp)/(sum(ivarfb_counts$both_fp)+sum(ivarfb_counts$both_tp))## [1] 0.04246795FPlayer_ivarfb = ivarfb %>% filter(Category == "both_fp")
Othertype_ivarfb = ivarfb %>% filter(!Category == "both_fp")
Figivarfb = ggplot() +
geom_point(data= Othertype_ivarfb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
geom_point(data=FPlayer_ivarfb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
labs(x="ivar", y= "freebayes") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 73.2%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 4.2%", hjust = "left")## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: widthprint(Figivarfb)## Warning: Removed 49 rows containing missing values (geom_point).
ggsave(Figivarfb,
filename = glue("{workdirectory}/figures_new/Figivarfb.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 49 rows containing missing values (geom_point).ggsave(Figivarfb,
filename = glue("{workdirectory}/figures_pdf/Figivarfb.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 49 rows containing missing values (geom_point).#ivar vs varscan
ivarvarscan = merge(ivarfreq, varscanfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
ivarvarscan = ivarvarscan%>%filter(!Copy_number == "control")
ivarvarscan$type.x[is.na(ivarvarscan$type.x)] <- "NA"
ivarvarscan$type.y[is.na(ivarvarscan$type.y)] <- "NA"
ivarvarscan = ivarvarscan %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
ivarvarscan_bothtp = ivarvarscan %>% filter(Category == "both_tp")
#calculate both FP%
ivarvarscan_counts = ivarvarscan %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
ivarvarscan_counts$both_tp[is.na(ivarvarscan_counts$both_tp)] = 0
ivarvarscan_counts$both_fp[is.na(ivarvarscan_counts$both_fp)] = 0
ivarvarscan_counts$both_fn[is.na(ivarvarscan_counts$both_fn)] = 0
sum(ivarvarscan_counts$both_fp)/(sum(ivarvarscan_counts$both_fp)+sum(ivarvarscan_counts$both_tp))## [1] 0.01021152FPlayer_ivarvarscan = ivarvarscan %>% filter(Category == "both_fp")
Othertype_ivarvarscan = ivarvarscan %>% filter(!Category == "both_fp")
Figivarvarscan = ggplot() +
geom_point(data= Othertype_ivarvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
geom_point(data=FPlayer_ivarvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
labs(x="ivar", y= "varscan") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 83.1%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 1.02%", hjust = "left")## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: widthprint(Figivarvarscan)## Warning: Removed 45 rows containing missing values (geom_point).
ggsave(Figivarvarscan,
filename = glue("{workdirectory}/figures_new/Figivarvarscan.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 45 rows containing missing values (geom_point).ggsave(Figivarvarscan,
filename = glue("{workdirectory}/figures_pdf/Figivarvarscan.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 45 rows containing missing values (geom_point).#hc vs freebayes
hcfb = merge(hcfreq, freebayesfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
hcfb = hcfb%>%filter(!Copy_number == "control")
hcfb$type.x[is.na(hcfb$type.x)] <- "NA"
hcfb$type.y[is.na(hcfb$type.y)] <- "NA"
hcfb = hcfb %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
hcfb_bothtp = hcfb %>% filter(Category == "both_tp")
#calculate both FP%
hcfb_counts = hcfb %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
hcfb_counts$both_tp[is.na(hcfb_counts$both_tp)] = 0
hcfb_counts$both_fp[is.na(hcfb_counts$both_fp)] = 0
hcfb_counts$both_fn[is.na(hcfb_counts$both_fn)] = 0
sum(hcfb_counts$both_fp)/(sum(hcfb_counts$both_fp)+sum(hcfb_counts$both_tp))## [1] 0.01821336Fighcfb = ggplot(hcfb, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category)) +
labs(x="hc", y= "freebayes") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 69.4%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 1.82%", hjust = "left")## Warning: Ignoring unknown parameters: widthprint(Fighcfb)## Warning: Removed 1590 rows containing missing values (geom_point).
ggsave(Fighcfb,
filename = glue("{workdirectory}/figures_new/Fighcfb.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 1590 rows containing missing values (geom_point).ggsave(Fighcfb,
filename = glue("{workdirectory}/figures_pdf/Fighcfb.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 1590 rows containing missing values (geom_point).#hc vs varscan
hcvarscan = merge(hcfreq, varscanfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
hcvarscan = hcvarscan%>%filter(!Copy_number == "control")
hcvarscan$type.x[is.na(hcvarscan$type.x)] <- "NA"
hcvarscan$type.y[is.na(hcvarscan$type.y)] <- "NA"
hcvarscan = hcvarscan %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
hcvarscan_bothtp = hcvarscan %>% filter(Category == "both_tp")
#calculate both FP%
hcvarscan_counts = hcvarscan %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
hcvarscan_counts$both_tp[is.na(hcvarscan_counts$both_tp)] = 0
hcvarscan_counts$both_fp[is.na(hcvarscan_counts$both_fp)] = 0
hcvarscan_counts$both_fn[is.na(hcvarscan_counts$both_fn)] = 0
sum(hcvarscan_counts$both_fp)/(sum(hcvarscan_counts$both_fp)+sum(hcvarscan_counts$both_tp))## [1] 0.0084246Fighcvarscan = ggplot(hcvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category)) +
labs(x="hc", y= "varscan") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 72.1%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 0.84%", hjust = "left")## Warning: Ignoring unknown parameters: widthprint(Fighcvarscan)## Warning: Removed 1530 rows containing missing values (geom_point).
ggsave(Fighcvarscan,
filename = glue("{workdirectory}/figures_new/Fighcvarscan.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 1530 rows containing missing values (geom_point).ggsave(Fighcvarscan,
filename = glue("{workdirectory}/figures_pdf/Fighcvarscan.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 1530 rows containing missing values (geom_point).#fb vs varscan
fbvarscan = merge(freebayesfreq, varscanfreq,
by.x =c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"),
by.y = c("POS","CHROM", "REF", "ALT", "Expected_freq", "Copy_number", "Rep"), all = T)
fbvarscan = fbvarscan%>%filter(!Copy_number == "control")
fbvarscan$type.x[is.na(fbvarscan$type.x)] <- "NA"
fbvarscan$type.y[is.na(fbvarscan$type.y)] <- "NA"
fbvarscan = fbvarscan %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == type.y & type.x == 'FN', "both_fn",
ifelse(type.x == "TP" & type.y != "TP", "caller1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'caller2_tp',
ifelse(type.x == 'FP' & type.y == 'NA' | type.x == 'NA' & type.y == 'FP', 'single_fp',
ifelse(type.x == 'FN' & type.y != 'FN' | type.x != 'FN' & type.y == 'FN', 'single_fn',
"NA"))))))))
#calculate both TP%
fbvarscan_bothtp = fbvarscan %>% filter(Category == "both_tp")
#calculate both FP%
fbvarscan_counts = fbvarscan %>% group_by(Expected_freq, Copy_number, Category) %>% add_tally(name = 'type_count') %>% ungroup() %>%select(Expected_freq, Category,type_count, vcf_inputs.x, vcf_inputs.y, Copy_number) %>% unique() %>% pivot_wider(names_from = Category, values_from = type_count)
fbvarscan_counts$both_tp[is.na(fbvarscan_counts$both_tp)] = 0
fbvarscan_counts$both_fp[is.na(fbvarscan_counts$both_fp)] = 0
fbvarscan_counts$both_fn[is.na(fbvarscan_counts$both_fn)] = 0
sum(fbvarscan_counts$both_fp)/(sum(fbvarscan_counts$both_fp)+sum(fbvarscan_counts$both_tp))## [1] 0.01125541FPlayer_fbvarscan = fbvarscan %>% filter(Category == "both_fp")
Othertype_fbvarscan = fbvarscan %>% filter(!Category == "both_fp")
Figfbvarscan = ggplot() +
geom_point(data= Othertype_fbvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
geom_point(data=FPlayer_fbvarscan, aes(x = ALT_FREQ.x, y = ALT_FREQ.y, color = Category), width = 0.2, alpha = 0.4) +
labs(x="freebayes", y= "varscan") +
geom_point(width = 0.2, alpha = 0.5) +
category_colScale_1 +
theme_bw()+
theme(axis.title = element_text(size = 15))+
theme(legend.text = element_text(size = 15))+
annotate(geom = "text", x = 0.02, y = 0.85, label = "%TP = 70.0%", hjust = "left")+
annotate(geom = "text", x = 0.02, y = 0.8, label = "%FP = 1.13%", hjust = "left")## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: width
## Warning: Ignoring unknown parameters: widthprint(Figfbvarscan)## Warning: Removed 88 rows containing missing values (geom_point).
ggsave(Figfbvarscan,
filename = glue("{workdirectory}/figures_new/Figfbvarscan.png"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 88 rows containing missing values (geom_point).ggsave(Figfbvarscan,
filename = glue("{workdirectory}/figures_pdf/Figfbvarscan.pdf"),
width = 5,
height = 4, limitsize=FALSE)#, useDingbats = FALSE)## Warning: Removed 88 rows containing missing values (geom_point).How does having cutoffs affect variant calling? - Fig S7B,S7C, Fig 4C & 4D
#Construct cutoff df
#Loop through a vector of frequency cutoffs and read depth cutoffs
freq_list = c(0, 0.01, 0.02, 0.03)
rd_list = c(0, 100, 200, 300)
vdf_filt = data.frame()
for(f in freq_list){
#print(f)
for(c in rd_list){
#print(c)
#print(dim(filt_vdf))
fv = vcf_plus %>%
mutate(new_category = ifelse(ALT_FREQ >= f & gt_DP >= c & type == 'TP',
"TP",
ifelse(ALT_FREQ < f & type == 'TP'|
gt_DP < c & type == 'TP',
"FN",
ifelse(type == 'FN',
"FN",
ifelse(type == 'FP' & ALT_FREQ >= f & gt_DP >= c,
"FP", "TN")))))
fv$freq_cut = f
fv$cov_cut = c
vdf_filt = rbind(vdf_filt, fv)
}
}
dim(vdf_filt)## [1] 520672 47#colnames(vdf_filt)
vdf_filt$category = vdf_filt$new_category
#calculate the number of TP, FP, FN after filtering
message("Category count for filt data")## Category count for filt datavdf_filt = vdf_filt %>% ungroup() %>% unique()
group_columns = c('category',"vcf_inputs",'freq_cut','cov_cut', "Expected_freq", "Copy_number", "Rep")
count_filt = vdf_filt %>%
group_by(across(all_of(group_columns))) %>%
add_tally(name = 'category_count') %>%
ungroup() %>%
select(all_of(c(group_columns, 'category_count'))) %>%
unique()
# Load function: adjust_count
adjust_counts = function(count_df){
count_df = count_df %>%
pivot_wider(names_from = category, values_from = category_count)
if (!"FP" %in% colnames(count_df)){
print("No false-positives - adjusting")
count_df$FP = 0
}else{print("FP present - no adjustment needed")}
count_df[is.na(count_df)] = 0
count_df$TPR = count_df$TP/(count_df$TP + count_df$FN)
count_df$PPV = count_df$TP/(count_df$TP + count_df$FP)
count_df$FNR = count_df$FN/(count_df$FN + count_df$TP)
count_df$FDR = count_df$FP/(count_df$FP + count_df$TP)
count_df$F1 = 2 * ((count_df$PPV * count_df$TPR)/(count_df$PPV + count_df$TPR))
count_df[is.na(count_df)] = 0
#count_df$gt_DP = as.numeric(as.character(count_df$gt_DP))
return(count_df)
}
# put that count dataframe into the 'adjust_counts' function
message("Adjust filtered count df")## Adjust filtered count dfdf_filt = adjust_counts(count_filt)## [1] "FP present - no adjustment needed"df_filt = df_filt %>% filter (cov_cut == "0", Rep == "rep1") %>% group_by(cov_cut, freq_cut, vcf_inputs, Expected_freq, Copy_number, Rep) %>% mutate(TP_percentage = TP/(TP + FN + FP), FP_percentage = FP/(TP + FN + FP), FN_percentage = FN/(TP + FN + FP)) %>% unique() %>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_TP = mean(TP_percentage), sd_TP = sd(TP_percentage))%>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_FP = mean(FP_percentage), sd_FP = sd(FP_percentage))%>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_FN = mean(FN_percentage), sd_FN = sd(FN_percentage))
df_filt = df_filt %>% filter(Copy_number != "control")
df_filt$freq_cut = as.character(df_filt$freq_cut)
#update replicates df with new SNV_info
rep1 = vcf_plus %>% filter(Rep == "rep1") %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))
rep2 = vcf_plus %>% filter(Rep == "rep2") %>% filter(!FerretID %in% c("Mix37", "Mix38", "Mix39", "Mix40", "Mix41", "Mix42", "Mix44"))
# merge the replicates
replicates = merge(rep1, rep2,
by.x =c('CHROM', "Copy_number", "POS", "Expected_freq", "REF", "ALT", "ChromKey", "vcf_inputs", "Use", "Cohort", "repname"),
by.y = c('CHROM', "Copy_number", "POS", "Expected_freq", "REF", "ALT", "ChromKey", "vcf_inputs", "Use", "Cohort", "Sample"), all = T)
#Change NA to zero
replicates$ALT_FREQ.x[is.na(replicates$ALT_FREQ.x)] = 0
replicates$ALT_FREQ.y[is.na(replicates$ALT_FREQ.y)] = 0
replicates$type.x[is.na(replicates$type.x)] = "NONE"
replicates$type.y[is.na(replicates$type.y)] = "NONE"
# Remove the controls for this analysis
replicates = replicates %>% filter(!Copy_number == "control")
# specify the four categories
replicates = replicates %>% mutate(Category = ifelse(type.x == 'TP' & type.x == type.y, "both_tp",
ifelse(type.x == type.y & type.x == 'FP', "both_fp",
ifelse(type.x == "TP" & type.y != "TP", "rep1_tp",
ifelse(type.x != "TP" & type.y == 'TP', 'rep2_tp',
ifelse(type.x == 'FN' & type.x == type.y, "both_fn",
ifelse(type.x == 'FP' & type.y != 'FP' | type.x != 'FP' & type.y == 'FP', 'single_fp', "NA")))))))
across_replicates = replicates %>% filter(Category == "both_tp" | Category =="both_fp" |Category =="both_fn")
#Count the number of TP, FN, FP
type_counts_two_rep = across_replicates %>% group_by(Expected_freq, Category, vcf_inputs, Copy_number, CHROM) %>% add_tally(name = 'type_count') %>% ungroup() %>% select(Expected_freq, Category,type_count, vcf_inputs, Copy_number, CHROM) %>% unique()
#make sure for each expected freq + copy number set, the sum of TP & FN is the same (becuase combined they are the total number of SNVs)
type_counts_two_rep = type_counts_two_rep %>% pivot_wider(names_from = Category, values_from = type_count)
#type_counts_individual_rep[is.na(type_counts_individual_rep)] = 0
type_counts_two_rep$both_fp[is.na(type_counts_two_rep$both_fp)] = 0
type_counts_two_rep$both_tp[is.na(type_counts_two_rep$both_tp)] = 0
type_counts_two_rep = across_replicates %>% group_by(Expected_freq, Category, vcf_inputs, Copy_number) %>% add_tally(name = 'type_count') %>% ungroup() %>% select(Expected_freq, Category,type_count, vcf_inputs, Copy_number) %>% unique()
#make sure for each expected freq + copy number set, the sum of TP & FN is the same (becuase combined they are the total number of SNVs)
type_counts_two_rep = type_counts_two_rep %>% pivot_wider(names_from = Category, values_from = type_count)
#type_counts_individual_rep[is.na(type_counts_individual_rep)] = 0
type_counts_two_rep$both_fp[is.na(type_counts_two_rep$both_fp)] = 0
type_counts_two_rep$both_tp[is.na(type_counts_two_rep$both_tp)] = 0
#type_counts_individual_rep = type_counts_individual_rep %>% group_by(Expected_freq,vcf_inputs) %>% mutate(SNV_count = both_fn + both_tp)
type_counts_two_rep["Rep"] = "Merged"
colnames(type_counts_two_rep)[4] <- "FN"
colnames(type_counts_two_rep)[5] <- "TP"
colnames(type_counts_two_rep)[6] <- "FP"
#Calculate TP percentage and FP percentage
type_counts_two_rep = type_counts_two_rep %>% group_by(vcf_inputs, Expected_freq, Copy_number) %>% mutate(TP_percentage = TP/(TP + FN + FP), FP_percentage = FP/(TP + FP), FN_percentage = FN/(TP + FN)) %>% unique() #%>% group_by(Copy_number, vcf_inputs) %>% mutate(Mean_TP = mean(TP_percentage), sd_TP = sd(TP_percentage))%>% group_by(Copy_number, vcf_inputs) %>% mutate(Mean_FP = mean(FP_percentage), sd_FP = sd(FP_percentage))%>% group_by(Copy_number, vcf_inputs) %>% mutate(Mean_FN = mean(FN_percentage), sd_FN = sd(FN_percentage))
type_counts_two_rep$FP_percentage[is.na(type_counts_two_rep$FP_percentage)] = 0
type_counts_two_rep$FN_percentage[is.na(type_counts_two_rep$FN_percentage)] = 0
FigS7B = ggplot()+
geom_line(data = df_filt %>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
aes(x=Expected_freq,
y = FDR,
group = interaction(freq_cut, Copy_number),
linetype = freq_cut,
color = vcf_inputs), alpha = 0.8, size = 1) +
geom_point(data=df_filt%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
aes(x=Expected_freq, y=FDR,
colour = vcf_inputs, shape = Copy_number),
alpha = 0.9, size = 2) +
geom_line(data = type_counts_two_rep%>% filter( Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
aes(x=Expected_freq, y= FP_percentage,
group = interaction(Rep, Copy_number)),
color = 'black',
alpha = 0.8)+
geom_point(data=type_counts_two_rep%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
aes(x=Expected_freq, y= FP_percentage, shape = Copy_number,),
color = 'black',
alpha = 0.9)+
tool_colScale +
#labs(x="Copy Number", y= "FDR") +
theme_bw() +
facet_grid(Copy_number~vcf_inputs) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS7B)
ggsave(FigS7B,
filename = glue("{workdirectory}/figures_pdf_new/FigS7B.pdf"),
width = 9,
height = 5, limitsize=FALSE, useDingbats = FALSE)
FigS7B_2 = ggplot()+
geom_line(data = df_filt %>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
aes(x=Expected_freq,
y = FDR,
group = interaction(freq_cut, Copy_number),
linetype = freq_cut,
color = vcf_inputs), alpha = 0.8, size = 1) +
geom_point(data=df_filt%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
aes(x=Expected_freq, y=FDR,
colour = vcf_inputs, shape = Copy_number),
alpha = 0.9, size = 2) +
geom_line(data = type_counts_two_rep%>% filter( Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
aes(x=Expected_freq, y= FP_percentage,
group = interaction(Rep, Copy_number)),
color = 'black',
alpha = 0.8)+
geom_point(data=type_counts_two_rep%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
aes(x=Expected_freq, y= FP_percentage, shape = Copy_number,),
color = 'black',
alpha = 0.9)+
tool_colScale +
#labs(x="Copy Number", y= "FDR") +
theme_bw() +
facet_grid(Copy_number~vcf_inputs) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS7B_2)
ggsave(FigS7B_2,
filename = glue("{workdirectory}/figures_pdf_new/FigS7B_2.pdf"),
width = 7,
height = 5, limitsize=FALSE, useDingbats = FALSE)
FigS7C = ggplot()+
geom_line(data = df_filt %>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
aes(x=Expected_freq,
y = FNR,
group = interaction(freq_cut, Copy_number),
linetype = freq_cut,
color = vcf_inputs), alpha = 0.8, size = 1) +
geom_point(data=df_filt%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
aes(x=Expected_freq, y=FNR,
colour = vcf_inputs, shape = Copy_number),
alpha = 0.9, size = 2) +
geom_line(data = type_counts_two_rep%>% filter( Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
aes(x=Expected_freq, y= FN_percentage,
group = interaction(Rep, Copy_number)),
color = 'black',
alpha = 0.8)+
geom_point(data=type_counts_two_rep%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("freebayes", "ivar", "timo", "varscan")),
aes(x=Expected_freq, y= FN_percentage, shape = Copy_number,),
color = 'black',
alpha = 0.9)+
tool_colScale +
#labs(x="Copy Number", y= "FDR") +
theme_bw() +
facet_grid(Copy_number~vcf_inputs) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS7C)
ggsave(FigS7C,
filename = glue("{workdirectory}/figures_pdf_new/FigS7C.pdf"),
width = 9,
height = 5, limitsize=FALSE, useDingbats = FALSE)
FigS7C_2 = ggplot()+
geom_line(data = df_filt %>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
aes(x=Expected_freq,
y = FNR,
group = interaction(freq_cut, Copy_number),
linetype = freq_cut,
color = vcf_inputs), alpha = 0.8, size = 1) +
geom_point(data=df_filt%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
aes(x=Expected_freq, y=FNR,
colour = vcf_inputs, shape = Copy_number),
alpha = 0.9, size = 2) +
geom_line(data = type_counts_two_rep%>% filter( Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
aes(x=Expected_freq, y= FN_percentage,
group = interaction(Rep, Copy_number)),
color = 'black',
alpha = 0.8)+
geom_point(data=type_counts_two_rep%>% filter(Copy_number %in% c("10^3", "10^6"), vcf_inputs %in% c("hc", "lofreq", "mutect2")),
aes(x=Expected_freq, y= FN_percentage, shape = Copy_number,),
color = 'black',
alpha = 0.9)+
tool_colScale +
#labs(x="Copy Number", y= "FDR") +
theme_bw() +
facet_grid(Copy_number~vcf_inputs) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS7C_2)
ggsave(FigS7C_2,
filename = glue("{workdirectory}/figures_pdf_new/FigS7C_2.pdf"),
width = 7,
height = 5, limitsize=FALSE, useDingbats = FALSE)
# Looking at 10^5 only
Fig4C = ggplot()+
geom_line(data = df_filt %>% filter( Copy_number == "10^5"),
aes(x=Expected_freq,
y = FDR,
group = freq_cut,
linetype = freq_cut,
color = vcf_inputs), alpha = 0.8, size = 1) +
geom_point(data=df_filt%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y=FDR,
colour = vcf_inputs),
alpha = 0.9, size = 2) +
geom_line(data = type_counts_two_rep%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y= FP_percentage,
group = Rep),
color = 'black',
alpha = 0.8)+
geom_point(data=type_counts_two_rep%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y= FP_percentage),
color = 'black',
alpha = 0.9)+
tool_colScale +
#labs(x="Copy Number", y= "FDR") +
theme_bw() +
facet_grid(.~vcf_inputs) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(Fig4C)
ggsave(Fig4C,
filename = glue("{workdirectory}/figures_pdf_new/Fig4C.pdf"),
width = 15,
height = 4, limitsize=FALSE, useDingbats = FALSE)
Fig4D = ggplot()+
geom_line(data = df_filt %>% filter( Copy_number == "10^5"),
aes(x=Expected_freq,
y = FNR,
group = freq_cut,
linetype = freq_cut,
color = vcf_inputs), alpha = 0.8, size = 1) +
geom_point(data=df_filt%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y=FNR,
colour = vcf_inputs),
alpha = 0.9, size = 2) +
geom_line(data = type_counts_two_rep%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y= FN_percentage,
group = Rep),
color = 'black',
alpha = 0.8)+
geom_point(data=type_counts_two_rep%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y= FN_percentage),
color = 'black',
alpha = 0.9)+
tool_colScale +
#labs(x="Copy Number", y= "FDR") +
theme_bw() +
facet_grid(.~vcf_inputs) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(Fig4D)
ggsave(Fig4D,
filename = glue("{workdirectory}/figures_pdf_new/Fig4D.pdf"),
width = 15,
height = 4, limitsize=FALSE, useDingbats = FALSE)FigS8C & S8D
df_filt = adjust_counts(count_filt)## [1] "FP present - no adjustment needed"df_filt = df_filt %>% filter(freq_cut == "0", Rep == "rep1") %>% group_by(cov_cut, freq_cut, vcf_inputs, Expected_freq, Copy_number, Rep) %>% mutate(TP_percentage = TP/(TP + FN + FP), FP_percentage = FP/(TP + FN + FP), FN_percentage = FN/(TP + FN + FP)) %>% unique() %>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_TP = mean(TP_percentage), sd_TP = sd(TP_percentage))%>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_FP = mean(FP_percentage), sd_FP = sd(FP_percentage))%>% group_by(Copy_number, vcf_inputs, freq_cut, cov_cut) %>% mutate(Mean_FN = mean(FN_percentage), sd_FN = sd(FN_percentage))
df_filt = df_filt %>% filter(Copy_number != "control")
df_filt$cov_cut = as.character(df_filt$cov_cut)
FigS8C = ggplot()+
geom_line(data = df_filt %>% filter( Copy_number == "10^5"),
aes(x=Expected_freq,
y = FDR,
group = cov_cut,
linetype = cov_cut,
color = vcf_inputs), alpha = 0.8, size = 1) +
geom_point(data=df_filt%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y=FDR,
colour = vcf_inputs),
alpha = 0.9, size = 2) +
geom_line(data = type_counts_two_rep%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y= FP_percentage,
group = Rep),
color = 'black',
alpha = 0.8)+
geom_point(data=type_counts_two_rep%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y= FP_percentage),
color = 'black',
alpha = 0.9)+
tool_colScale +
#labs(x="Copy Number", y= "FDR") +
theme_bw() +
facet_grid(.~vcf_inputs) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS8C)
ggsave(FigS8C,
filename = glue("{workdirectory}/figures_pdf_new/FigS8C.pdf"),
width = 15,
height = 4, limitsize=FALSE, useDingbats = FALSE)
FigS8D = ggplot()+
geom_line(data = df_filt %>% filter( Copy_number == "10^5"),
aes(x=Expected_freq,
y = FNR,
group = cov_cut,
linetype = cov_cut,
color = vcf_inputs), alpha = 0.8, size = 1) +
geom_point(data=df_filt%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y=FNR,
colour = vcf_inputs),
alpha = 0.9, size = 2) +
geom_line(data = type_counts_two_rep%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y= FN_percentage,
group = Rep),
color = 'black',
alpha = 0.8)+
geom_point(data=type_counts_two_rep%>% filter( Copy_number == "10^5"),
aes(x=Expected_freq, y= FN_percentage),
color = 'black',
alpha = 0.9)+
tool_colScale +
#labs(x="Copy Number", y= "FDR") +
theme_bw() +
facet_grid(.~vcf_inputs) +
theme(legend.key = element_blank(),
strip.background = element_rect(colour="black", fill="white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
print(FigS8D)
ggsave(FigS8D,
filename = glue("{workdirectory}/figures_pdf_new/FigS8D.pdf"),
width = 15,
height = 4, limitsize=FALSE, useDingbats = FALSE)Fig3B
FP = vcf_plus %>% filter(type == "FP", Copy_number != "control")
FP%>% filter(ALT_FREQ>0.75)## [1] POS CHROM REF
## [4] ALT Copy_number Expected_freq
## [7] vcf_inputs Rep filename
## [10] ChromKey ID REF_COUNT
## [13] ALT_COUNT gt_DP sample
## [16] REF_FREQ ALT_FREQ ALT_TYPE
## [19] majorfreq minorfreq major
## [22] minor CHROM_SIZE GENOME_SIZE
## [25] LibraryPosition SampleInfo Use
## [28] Cohort FerretID Sample
## [31] repname MRTPCR_Date MTRPCR_Plate
## [34] PostCleanUpConc PostAmpConc PostDilutionConc
## [37] i5 i5_Tuboweb i7
## [40] i7_TuboWeb Adaptor.IDs TrueExpectedCopyNumber
## [43] TrueExpectedFrequency type
## <0 rows> (or 0-length row.names)PlotTheme1 = theme_bw() +
theme(legend.key = element_blank(),
strip.background = element_rect(colour= "black", fill= "white"),
axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
plot3b1 = ggplot(FP, aes(x=ALT_FREQ, y = gt_DP, color = vcf_inputs)) +
geom_point(alpha = 0.8, size = 2) +
tool_colScale +
PlotTheme1 +
geom_hline(yintercept = 500, linetype = 2, color = 'black') +
geom_vline(xintercept = 0.03, linetype = 2, color = 'black') +
theme(legend.position = 'NONE') +
labs(x="allele frequency", y = 'read depth')
print(plot3b1)
ggsave(plot3b1,
filename = glue("{workdirectory}/figures_pdf_new/Fig3B1_flu_synthetic.pdf"),
width = 4,
height = 4, limitsize=FALSE, useDingbats = FALSE)
plot3b2 = ggplot(FP, aes(x=gt_DP, fill = vcf_inputs)) +
geom_histogram(binwidth = 500) +
tool_colScale_fill +
PlotTheme1 +
theme(legend.position = 'NONE') +
labs(x="read depth", y= "false positive count") +
# facet_grid(.~vcf_inputs) +
coord_flip() +
scale_x_continuous(position = "top")
print(plot3b2)
ggsave(plot3b2,
filename = glue("{workdirectory}/figures_pdf_new/Fig3B2_flu_synthetic.pdf"),
width = 2,
height = 4, limitsize=FALSE, useDingbats = FALSE)
plot3b3 = ggplot(FP, aes(x=ALT_FREQ, fill = vcf_inputs)) +
geom_histogram(binwidth = 0.02) +
tool_colScale_fill +
PlotTheme1 +
theme(legend.position = 'NONE') +
labs(x="allele frequency", y = 'false positive count')+
scale_x_continuous(position = "top")
print(plot3b3)
ggsave(plot3b3,
filename = glue("{workdirectory}/figures_pdf_new/Fig3B3_flu_synthetic.pdf"),
width = 4,
height = 2, limitsize=FALSE, useDingbats = FALSE)